Maybe it's that when you learn to use a hammer, everything looks like a nail, so I might be over-diagnosing this, but it strikes me that this issue and hostilities between theists and atheists has, at it's core, psychological concept called out-grouping. There is also more than a chance I'm using the term incorrectly, but I hopefully explain the concept well enough.
Us humans form groups we identify in, all probably a result of tribes we originally lived in. We empathize with the people in our groups(us), but we push back on those not in the groups(them). Those who are out-grouped often are viewed very one-dimensional, and often with hostility. Without a cogniscience of this effect, it can get rampantly out of hand. Just look how conservatives view liberals and liberals view conservatives. How Christians view Atheists and Atheists view Christians. Star Wars nerds view Star Trek nerds and how Star Trek nerds know that Star Wars nerds are really soft sci-fi at best and more pop culture than nerdcore. American's viewing foreigners as un-free, socialistic, poor, whatever, and foreigners viewing Americans as fat, stupid, lazy, redneck, greedy, culturally insensitive, and pretentious.
You see my own effects of out-grouping? Never mind the Star Wars/Star Trek thing. That's fact. But rather, I separated groups by "American" and "not American." Rationally, I know the concept that rest of the world is homogenized in their attitudes towards American is woefully flawed, but at a very basic level, I do see it that way.
Similar effects even happen geographically. The land closer to you, you visualize bigger. I remember at a business trip to VA, I was under the impression that the distance between Boston and Arlington/Washington D.C was maybe 2-3 hours. It's more like twice that, apparently. But, the east cost just seems smaller and compacted to my view. Likewise, my coworkers commented that it's not uncommon for them to think that the distance between L.A and San Francisco is around 3 hours. For those who don't know, it's more like 7.
Any group that people identify with and in, you're likely to see this affect. Race. Politics. Nationality. Game systems. And yes, oh yes, Religion.
It's more than likely that Religion exacerbates this affect. In just another thread, someone showed genuine concern over a couple religions working together to combat slavery. How is this a bad thing? It's not. Is this person bad or stupid? No, of course not. But the teachings he read led him to hold these cautions against working with others. I empathize because I remember feeling that way and more. I felt that any inter-religious activity was a way to undermine God. What does light have in common with darkness? Don't be unequally yoked. I remember scriptural teachings that actively promoted a separation from all those not in your group. This is a core tenet among conservative Christianity, and in fact, most religions.
So when I, as an Atheist, criticize religion, it often comes down to this. It's not that religion is inherently evil, but just as it can promote positive teachings, it can also promote negative behaviors.
I'm not asking you to throw away your religion, that's for another conversation

Let me start small within denominations. We have a couple Mormons on the board and I think we're all better for it. Discrimination at the hand of other Christians is very core in their history. It's why they are based in Utah and not a more easterly state. And even now, when people think about Mormons, they first thing that comes to mind is probably door-to-door preachers with white shirts, black slacks, black ties, and a bike helmet. And it often stops at that. But these are real people. Hopes. Dreams. Fears. Doubts. Passions. How can that ever be the end of the concept of man or a woman, and how can you define an entire community that way? But their outgrouped and so they are. It's often not until you start befriended someone of that outgroup do you realize they aren't so out after all.
I've seen a ton of people change their tone about homosexuals after they made friends. The Queer movement might have put homosexuality on the public map, but it made it weird and outgrouped for so many people. It's that chill gay friend that really makes you think about whether gay marriage should or should not be legal. Not addressing religious teachings on homosexuality, but it's an effect I've seen.
Back to Mormonism, as they are often out-grouped, this leads to a de-empathizing with them. How else can someone openly ridicule them with no guilt? Or drive them from their homes (in days of olde). Because they aren't thought as real people, just cheap facsimiles. This happens the other way around, too, in strong Mormon communities. You don't think the Mormon church is domineering in SLC? It is.
This effect is even stronger and more prevalent between religions and non-religion. It's head-bangingly awful how so many people talk about each other and the images each paint are so farcical, so one-dimensionally bad, and so perspectively out of band, it's more like a preschool crayon drawing on a fridge than anything remotely realistic. And what's worse, some people only show that side.
It didn't take me long that the picture of atheists I got in church differed incredibly from the atheists I got to know, and also from the flaming ranters on, say, a common video sharing site. My long time as a Christian and still active involvement with fine folk as yourself makes these pictures I've seen from the aforementioned video site to be exactly what I described: out of perspective, one-dimensional, and farcical.
People are complex, not all are rich pools or introspective thought, but I think with closer inspection, you'll find that what was once perceived as an archetype of an outer group is really a vocal minority, and what's really behind that angry vocal minority is someone who's scared, hurt, or just gosh-darn-stupid. Yeah, that happens sometimes.
So, most of you are pretty spectacular when handling Atheists like myself, but I'd like to leave you with a couple thoughts:
1)We agree on all gods but one. If you feel like you can't understand why we don't believe in God, think about why you don't believe in Allah. Or Vishnu. Or Odin (Oro.. I get it). We probably agree with you.
2)For Christians in particular, you are taught to love your neighbor as yourself. I think this is a wonderful teaching and even better than it's presented as the core of the Law, as this sort of empathy is the core of morality. Not just love, but as yourself. The very essence of empathy. And we humans have an incredible capacity for empathy. We literally have a part of our brain built exactly for that. Look up Mirror Neurons. I feel like I'm falling back into Bible Study mode, but this is truly a great concept and I wish it was taken more to heart.
I'm not trying to Biblical contradictions, although I am happy to discuss this elsewhere, but I would like if you could take a little time to contrast this to how "separation from the world" is taught. Can you truly love someone you disassociate with? Much less as yourself, when you view yourself as fundamentally different from them. Light and dark.
I don't mean to ask about what the Bible says. As you can guess, it doesn't matter to me. As I see it, It has some good writings, and it has some bad, and is an authority on none. I'll leave that stuff to you guys.
I want to know what you think is best. Is it best that you focus on separation or empathy.
(I do have a feeling this will lead to a discussion on how the two are not mutually exclusive. They are, though.)
3)Spend a little time on seeing where out grouping occurs in your life. We all do it, it's as natural as it comes. I'm not saying it's an evil thing either. It's important to have increased empathy and awareness in closer groups, like family and friends, and we are more likely incapable of extending this to the whole world. I do want to point out it's a dangerous thing. Just be aware. That's all for now.
Apologies for the WOT. If you made it this far, thanks for sticking through. It's no small investment and these thoughts are pretty important to me.