I think it is the pack mentality of our species. We group. That's our nature. And then those outside the group we are in are always somehow in a lesser group. It doesn't matter if its religion, Nationalism, or your bowling league. Its human nature.
In this case when believers are convinced that morality comes from their religion. It only makes sense that those who don't follow their belief must be morally vacant. Or that their only playing the game and aren't really rooted.

Even though the minute I say I believe in God somehow all of that changes.