Our very concept of morality is at the heart of this issue. While nontheists and progressive people of faith understand that morality is internal, we decide ourselves to do good, and we decide ourselves not to do bad, without the need for government or other higher powers to compel us to behave. Fundamentalists somehow feel they need government and God to keep a close watch on them to prevent them from going astray. If only everyone realized that you can be good without a god, and focused on developing empathy for others who we understand to be equal in worth to ourselves, and approached issues with compassion and reason, then we could finally come to an understanding and let people live as they see fit without harming others.
Hopefully a time will come where people can believe what they want to believe without telling others what they should believe or how they must behave. Until then, religious organizations need to be reminded occasionally that they are not the only ones deserving of protection and respect.