"annoyance at the threads I see where atheists are sniping at religious people and saying, "I'm just sticking up for the facts and fighting ignorance", when all you're doing is harm to your position in the eyes of the people you're supposedly trying to convince".
As an atheist who (I think) doesn't rudely dismiss people who disagree, I see what you're trying to say. As for the atheist / believer divide, there are certain memes that insensitive / ignorant people on both sides try to advance. I dislike it when atheists say believers don't or won't use their brains, and I also dislike it when believers say atheists cannot be moral people and try to make it appear that atheists are some kind of organized religion. (Atheists can be moral people - Bill Gates and Warren Buffett are wonderfully charitable billionaires who are definitely nonreligious and possibly atheist.)
Atheists are still a picked-on minority. The zeal of a vocal segment of believers to try to demonize/discredit them show the worst side of religious belief. That treatment and that kind of marginalization (sometimes enforced by law) leads a few atheists to seem quite militant - an attempt to match the intensity of the other side.
Personally my secular humanism is more of a live-and-let-live type of approach. There are good, thinking, caring people on both sides of the believer / skeptic divide. Goodness or thinking ability is not the sole possession of one or the other side.