I think the reason for that is the country was founded by Christians. But you're right, they did found it on the idea of religious freedom. And I can totally see what you're saying, because most Americans don't know anything outside of the bubble we're put in.
But it seems like in a country that is suppose to be religously "free" there is a lot of controversy on how that should actually work. I think it's dumb to worry about the politics of it, because that will just set everyone into a circle of arguing and not moving forward with the issue.