I've been thinking about this and this is really the fundamental problem about religion. People can say oh religion atheism it's both kind of the same, you know ultimately people have things that they want and things that they think are right or wrong, etc etc.
The difference is religion has an intrinsically built-in mandate that you can't just think that this is right or wrong for you, but right or wrong for everyone. This intrinsically leads to the conclusion that others must be forced to comply with your standards, even if it doesn't affect you. Religion can never become pacified or progressive enough for this not to be a problem, as it comes from the fact that religion posits an absolute external morality. If you have a religious group and an atheist group, the atheist group could conceivably leave the religious group in peace to do what they want to do forever (although let's be honest that isn't very likely either because people are people). But the only way that a religious group could leave some other group whether atheist or not in peace to do what they want forever, would only be if they never realized the mandate that is logically implied by their belief system. Essentially, the most harmless religious group is one that hasn't thought too hard about it yet. A religious group, by it's very nature, cannot be content with leaving others alone to live differently from them.