From the reddit /r/atheism FAQ...
"There's a fundamental battle between rationality and supernaturalism, between a worldview based around evidence and facts and one based around faith and superstition. That's the tension between theism and atheism, more so than any actual evil committed in the name of any god. Even if no atrocities or great social injustices have ever been committed in the name of your religion, if there's still zero evidence in favour of your claims, your religion isn't any more credible.
A strongly held belief in the Santa Claus is mostly harmless, and may well help you to be a more generous person, but it still requires you to ignore or rationalize away huge piles of evidence in order to maintain. This sort of Faith requires a suspension of the part of your brain responsible for telling sense from nonsense, and if you're willing to let something so huge as a God Claim through unchallenged, who knows what else might slip through the cracks? Once you admit that you believe in something "because of faith", you are essentially admitting that you don't care whether or not it is actually true. As soon as you stop caring about reality in one aspect of your life, it becomes that much easier to stop caring about reality in others.
The problem isn't specifically a hatred of gays/women/blacks/etc., or an opposition to Cosmology or Biology. The problem is delusion, dogma, and a willingness to ignore reality that one finds inconvenient. As far as most skeptics are concerned, people who believe uncritically in supernaturalist religion, who are willing to continue believing in extraordinary claims despite the complete lack of evidence, have a fundamentally dishonest worldview that can never fully coincide with evidence and rationality.
Furthermore, anyone who demands respect for uncritical acceptance of superstitious nonsense, even mostly harmless nonsense, is indirectly giving aid and comfort to the fundamentalists, because they're making it that much less acceptable to criticize those who hold similar beliefs which are obviously crazy or evil.
It's nice that some religious people share some political opinions with some atheists. It's nice that some religious people don't hate gay people, it's nice that some religious people accept evolution, it's nice that some religious people accept that the Big Bang happened. Heck, it's nice that most religious people are willing to accept that the Earth isn't flat. It's certainly better than the alternative.
But if you think those things are all that we take issue with, or that those are the only things wrong with theism or religion, then you're missing the point.
So, yes, we know you're not as bad as those crazies. But unless you're opposed to all of the things wrong with religion, don't be surprised if you're seen as part of the problem."
