Because St Thomas Aquinas believed in a kind of human dominion over animals that suggested humanity could, in general, use them as they wish, he had to explain why God would take care to include laws in the Torah which forbade various forms of animal cruelty. His answer was simple: God was forming a good habit in them, that which would lead them not only to not be cruel to animals, but to their fellow humans. If they learned to be sympathetic to animals, they would be sympathetic to the pains of their neighbor:
Now it is evident that if a man practice a pitiful affection for animals, he is all the more disposed to take pity on his fellow-men: wherefore it is written (Proberts 11:10): ‘The just regardeth the lives of his beasts: but the bowels of the wicked are cruel.’ Consequently the Lord, in order to inculcate pity to the Jewish people, who were prone to cruelty, wished them to practice pity even with regard to dumb animals, and forbade them to do certain things savoring of cruelty to animals.
While it might be prudent not to limit God’s intent to this one purpose, St Thomas does bring up a good point: how we treat animals often ends up reflected in how we treat each other. This is one of the reasons why many moral philosophers interested in the issue of animals and our treatment of them think that animal suffering, especially suffering imposed upon them by humanity, matters.
If we want to produce a more virtuous society, we must look at those activities which produce the virtues and support them, and look at those activities which produce vices, and discourage (or forbid) them. Even if one is not interested in animals as an ends in themselves, as creatures with their own worth given to them by God, one does not have to be disinterested in their maltreatment, but rather, one can find reasons to be concerned about our abuse of them. Indeed, this should make us stand back and reconsider what it is we say about out treatment of animals, and how we justify such actions. If we look at what we do, the justification often tends to be consequentialist, with the result that our justification for our treatment of animals reinforces a consequentialistic ethic in general. C.S. Lewis understood this — he understood that there had to be more justification given to our infliction of pain upon them than we see some sort of good end in our actions that justifies our means. Otherwise, as he pointed out, we will not end with such treatment with animals but with compartmentalizing various parts of human society who can be justly abused for the sake of another: “If a mere sentiment justifies cruelty, why stop at a sentiment for the whole human race? There is also a sentiment for the white man against the black, for a Herrenvolk against the non-Aryans, for ‘civilized’ or ‘progressive’ people against ‘savages’ or ‘backward’ peoples. Finally, for our own country, party or class against others.”
We have come to see animals as merely tools for our will, to be used for our own good without considering the fact that they have their own proper end, their own proper good, which lies outside of our utilization. It does not take much to see how this has trained us to think about our activity consequentially, and therefore, why such thought continues even when discussing fellow humanity. This view of utility has, to be sure, been one of the many justifications which we can see throughout human history for our treatment of animals, though it historically has gone side by side with other considerations — ones which held some sway but over time have lost many of their adherents. For this reason, we find in modernity that consequential ethics has become the main justification of our treatment of other animals, leading us to naturally accept consequentialism unless we think it over and understand its defects.
It is important for us to see what other kinds of justifications have been used, and why they have been rejected, so that we can see how we got to the state we are today. Once we see that the issue of animals and their relationship to us has been with us for a long time, this will point out the need for us to continue such reflections today, and to continue with the task of purifying ourselves from erroneous worldviews.
Probably one of the worst justifications that have been given to justify any action we want upon animals is to suggest that they cannot suffer. There are many ways this has been done. Some, for example, have said that animals do not have any sense of memory beyond the present, or the ability to reason out and compare different states of being. In both of these situations, the conclusion was that this tells us animals cannot suffer because they do not have any comprehension of the pain, which is needed in order for the pain to rise up to the level of suffering. Or some, following Descartes, suggest not only that they are incapable of suffering, but that they cannot experience pain whatsoever. They are mere machines. Just because they appear to feel pain and suffer does not mean they are — we are misreading their experience and reading our experience into them. The problem with this argument is that it ends up removing the ability for us to prove the suffering of others. We can only be sure of our own suffering, and the rest of the world, even those who claim they are suffering, could be programmed to appear to suffer without actually suffering. If we cannot trust analogy to suggest suffering in animals, we cannot trust analogy to suggest suffering in others. If we presume that those who can speak are indeed going beyond some programmed response and therefore, we can trust them, this does not benefit those who are incapable of speaking for themselves, such as infants or those in a coma.  This is why it is important to not neglect the vulnerable and reject their suffering just because they cannot speak to us, because it is easy to apply the same standards to fellow humans and use those standards to deny them their own selfhood (as we see in debates over abortion, euthanasia, et. al.).
Probably the best justification which has been given has been based upon the authority which humanity has been given over nature. This is because there is truth behind this notion, though the problem comes from the way people interpret this truth. While the notion of human authority over the world can be developed out of Scripture (such as from Gen. 1:26), there has also been, to the side, a philosophical approach which led to this same conclusion. Humanity has natural control over the world, therefore, humanity has dominion — nature wills it, and so who are we to go against nature? Aristotle has helped promote this kind of reasoning through his Politics:
In like manner we may infer that, after the birth of animals, plants exist for their sake, and that the other animals exist for the sake of man, the tame for use and food, the wild, if not all at least the greater part of them, for food, and for the provision of clothing and various instruments. Now if nature makes nothing incomplete, and nothing in vain, the inference must be that she has made all animals for the sake of man.
Nonetheless, the problem with this idea is simple: control does not mean we can do everything we want over that which we control. Such a view leads not only to the justification of all kinds of instrumentalization of the world around us, but to our fellow humanity. We could look for qualities which suggest that we are superior to others and use that to justify dominion and abuse over those we consider to be our inferiors. Such an attitude, as Humphry Primatt points out, is unjustifiable:
Now, if amongst men, the differences of their powers of the mind, and of their complexion, stature, and accidents of fortune, do not give any one man a right to abuse or insult any other man on account of these differences; for the same reason, a man can have no natural right to abuse and torment a beast, merely because a beast has not the mental powers of a man. For, such as the man is, he is but as God made him; and the very same is true of the beast.
Authority over someone or something does not have to mean one is given absolute control over that which they hold authority. Rather, authority can be, and in contemporary Christian theology is seen as, a position of servitude. Authority over animals means we are to look after their wellbeing, just as those who are placed in positions of authority over other men and women are not to be seen as free to do as they wish over those same people, but rather, to work for the common good. This explains why the issue is not one of dominion itself, but the interpretation of dominion — it is not that we have to reject human authority in the world, but the way we see authority as a means to power.
Finally, the way abuse to animals has been, in one fashion or another, justified, has been through the so-called law of the jungle. Not only do we have the power to do as we wish (might makes right), but there is a constant struggle in creation, causing everything to fight against everything else. Animals can either be forced into submission to help us with our needs, or, if there is nothing we see in their value, they can be and should be eliminated before they harm us. While this kind of idea has been popular with some groups after Darwin, it predates him — we see it, for example, in the work of Hobbes:
We get a right over irrational creatures, in the same manner that we do over the persons of men; to wit, by force and natural strength. For if in the state of nature it is lawful for every one, by reason of that war which is of all against all, to subdue and also to kill men as oft as it shall seem to conduce unto their good; much more will the same be lawful against brutes; namely, at their own discretion to reduce those to servitude, which by art may be tamed and fitted for use, and to persecute and destroy the rest by a perpetual war as dangerous and noxious.
The pain and suffering of animals, especially when it is caused by us, should be a great concern for us. We can no longer just treat superiority as justification for evil. We must not allow ends to justify the means. We have to come to accept that pain is an evil, and an evil which must be taken seriously when we are its cause. And we must understand that, when it is done to an innocent, even to an innocent animal, without just cause, the deed can be said to be “Satanic.” Cardinal Newman pointed this out so very well:
I mean, consider how very horrible it is to read the accounts which sometimes meet us of cruelties exercised on brute animals. Does it not sometimes make us shudder to hear tell of them, or to read them in some chance publication which we take up? At one time it is the wanton deed of barbarous and angry owners who ill-treat their cattle, or beasts of burden; and at another, it is the cold-blooded and calculating act of men of science, who make experiments on brute animals, perhaps merely from a sort of curiosity. […]
Now what is it moves our very hearts, and sickens us so much at cruelty shown to poor brutes? I suppose this first, that they have done no harm; next, that they have no power whatever of resistance; it is the cowardice and tyranny of which they are the victims which makes their sufferings so especially touching. For instance, if they were dangerous animals, take the case of wild beasts at large, able not only to defend themselves, but even to attack us; much as we might dislike to hear of their wounds and agony, yet our feelings would be of a very different kind; but there is something so very dreadful, so satanic in tormenting those who never have harmed us, and who cannot defend themselves, who are utterly in our power, who have weapons neither of offence nor defence, that none but very hardened persons can endure the thought of it. 
The time has come for us to grow up spiritually, and to take our place in the world as its stewards. We must overcome our tendency to justify sin by unjust means. Our treatment of the world and what is contained within it changes us. The more virtue we show to the world, the better we become. The more selfish we are in our work, seeking to make everything an instrument of our will, the more sin finds its place in our heart and ends up destroying us even as we would destroy the world. While many of our former justifications for abuse have been overcome, the consequentialistic approach needs now to be full taken on and rejected. The habits involved in such behavior is leading to our own moral downfall. As C.S. Lewis and others properly point out, our actions to animals will quickly become our actions towards our fellow humanity. What we justify in one will become the justification for the other. Our arguments over abortion, torture, euthanasia, pornography, ecology, and the like all show this pernicious instrumentalist core as being behind our modern moral decay. Yes, there are differences to be had in creation. We are not all the same. It is what we do with those differences which are important. As Andrew Linzey points out, they do not have to lead to a denigration of the other: “Similarly, we have created an artificial distance between ourselves and other animals. We have seen that there are differences, sometimes important ones, both between and among species. It is not the citing of difference per see, but rather the denigration of difference that is questionable. It is how we use differences to justify unjust treatment, and specifically, how these are embodied in our language.” This is the challenge which lies before us. Consequentialism is rooted in our psyche, and often uses those very differences to justify itself. We now have to work to root it out. It will not be easy. But it is the only way we can go on if we want to continue to live together on this earth.
 cf., for example, St Thomas Aquinas, Summa Theologica. Trans. Fathers of the English Dominican Province (New York: Benziger Bros. edition, 1947), I q 96 a1.
 ibid., I-II. q102 a6 ad8.
 C.S. Lewis, “Vivisection” in Undeceptions. Ed. Walter Hooper (London: Geofrey Bless, 1971), 185. C.S. Lewis in this essay was arguing against the experimentation on live animals, and so the specific cruelty under discussion was vivisection, but the argument is sound beyond that one concrete example.
 See, for example, Andrew Linzey, Why Animal Suffering Matters (Oxford: Oxford University Press, 2009), 16-18.
 See Discourse V in Descartes’ Discourse on Method for his association of animals with machines.
 Angus Taylor makes this exact argument: “The pain and joy of others cannot be directly experienced, yet few of us doubt that other human beings can feel pain and joy. In large part this is because of the resemblances between their behaviour and our own. True, many (not all) other people can tell us in words how they feel; but how much confidence would we place in the words of a computer that insisted it was happy, or unhappy, and yet displayed no recognizable corresponding behaviour? That we can infer much about the inner life of animals on the basis of behavioural resemblances between them and human beings is affirmed by many,” Angus Taylor, Animals & Ethics (Orchard Park, NY: Broadview Press, 2003), 88-9.
 As an interesting aside, Macintyre suggests that analogies which exist between humanity and animals not only will allow us to better appreciate the inner-life of animals, but also ourselves: The silliness of Descartes’s insistence that nonhuman animals not only lack thoughts and intelligence, but also genuine perceptions and feelings has provided a salutary warning. But equally generally — there are rare and important exceptions — such philosophers seldom entertain the thought that the resemblances and analogies between the perceptions, feelings and intelligent activities of certain species of nonhuman animals might warrant, not only philosophical attention for their own sake, but also philosophical attention for the sake of a more adequate understanding of human perception, feeling and practical intelligence,” Alasdair Macintyre, Dependent Rational Animals: Why Human Beings Need the Virtues (Chicago: Open Court: 1999), 13.
 Aristotle, Politics in Introduction to Aristotle. Ed. Richard McKeon (New York: The Modern Library, 1947), 566. St. Thomas Aquinas, without surprise, follows Aristotle’s reasoning in his understanding of our relationship with animals, which shows that his interpretation of Genesis on dominion is through a hermeneutical lens which is not necessarily justified..
 Humphry Primatt, “The Duty of Mercy” in Animals and Christianity: A book of Readings. Ed. Andrew Linzey and Tom Regan (New York: Crossroad, 1988), 129.
 This comes from Jesus’ words, “If any one would be first, he must be last of all and servant of all” (Mark 9:35).
 Hobbes, ‘De Cive’ in Animal Rights. Ed. Andrew Linzey and Paul Barry Clarke (New York: Columbia University Press, 2004), 67.
 “Now, if pain is an evil, then the infliction of pain, considered in itself, must clearly be an evil act. But there are such things as necessary evils. Some acts which would be bad, simply in themselves, may be excusable and even laudable when they are necessary means to a greater good. In saying that the infliction of pain, simply in itself, is bad, we are not saying that pain ought never to be inflicted. Most of us think that it can rightly be inflicted for a good purpose — as in dentisty or just and reformatory punishment. The point is that it always requires justification,” C.S. Lewis, Vivisection, 183.
 John Henry Newman, ‘The Crucifixion’ (1842) in Parochial and Plain Sermons, vol 7. (New York: Longman, Green and Co., 1908), 136-7.
 Andrew Linzey, Why Animal Suffering Matters (Oxford: Oxford University Press, 2009), 44.