First, we have grown out of modern culture, and so have internalized many of its values. Diversity of points of view and the unavoidability of making choices of great importance while recognizing that others can make different choices, come naturally to most of us. We do not think that because someone made different choices that they therefore made inferior ones. Other religions can come to this conclusion as well of course, and practitioners of many, including many Christians, have done so. But for those whose past is in the pre-modern hierarchical world, this process is often a profound challenge that prompts considerable rethinking of assumptions long taken for granted.
Second, our spiritual practice sees and honors the sacred in this world, and not as some external force from on high. Science is how we study one dimension of the sacred. This view alone does not encourage science. Science is a mostly modern phenomenon. But when this view is added to a modern sensibility and within a modern society, the value and legitimacy of science emerges quite naturally.
The scientific atheist will ask us, "But don't you believe in Gods and Goddesses?" I am one who would answer a firm "Yes." And the atheist will then shake his or her head in disapproval. Doesn't that put us in the same bind as Christians who accepted science when it confirmed scripture and rejected it when it did not?
No, it does not.
First, a great many Pagans do not believe in such beings, whatever they may be, as being literally true. Significantly, they have little if any difficulty working with those of us who do, or we with them. Matters of theology do not, and so far as I can tell have never been fundamental issues within Pagan cultures. Understandings can vary and change without affecting the ways in which we gather together to honor contexts greater than we. NeoPaganism is a realm of extraordinary spiritual freedom and creativity.
Second, in my case and the cases of others I know who do take the Gods as real, our beliefs are based on direct experience, not an act of faith or commitment. We have personally encountered them. Consequently to call our views as "faith based" is to use a slippery term. Our position is quite different from the faith that is an act of commitment to a text. For example, in my view until someone has had such an experience, there is no very powerful reason to believe the Gods are real. I would never even imagine telling such a person "You need to have faith!"
The atheist's reply then might be "Well then, isn't your religion incoherent?"
Again there different responses we can make that I think eliminate the objection.
First, when the world itself is honored we can agree that life is a blessing, and that therefore the basic processes of life are also good. From that comes our Wheel of the Year, our emphasis on the feminine as well as the masculine, and on the goodness of material things. There is no clash here between a sensibility that experiences life as inspirited and one that does not, no more than between one that finds deserts beautiful and one that finds them desolate. In all these groups people can easily accept science as a means for learning about the world.
After listening to a prominent evolutionary scientist describe the beauty and wonder of the world, and his commitment to its flourishing, as well as describing his atheism, I asked him whether he might regard himself as a "nontheistic pantheist." He hesitated a moment to make sense of my unfamiliar terminology, and said, "Yes."
What distinguished him from me was a matter of personal inner experience. We agreed on virtually everything of importance in terms of how we viewed science and the knowledge it provided. We likely disagreed as to the extent in which consciousness exists within the material world and the nature of its relationship with matter. But those issues do not limit scientific inquiry or even discourage it.
Writing as a Wiccan, I think there is another dimension that ends the "war" between science and religion for Pagans. What unites us are not authoritative dogmas or even a weaker agreement as to what is real. What unites us is comfort in practicing together ways through which we honor what we each regard as a greater context of value and beauty. It is this greater context that gives our own lives a deeper and more embedded meaning. As we practice together our personal experiences fulfill us in this way, and the community of practice is a part of what makes this so. It is no big deal whether we understand this in the same way.
Science by its very nature does not access this realm of meaning. Inner significance can not be found in a measurement, prediction, or explanation of phenomena that make use only of mathematics, logic, and physical facts. Those are exterior to meaning, which refers to their inner significance, either for themselves or within a larger context.