I think another thing that causes division is our different approach. I saw this to a degree on a science thread.
As you pointed out, Palm, when atheists put scientific ideas out there, we welcome all the challenge in the room. Because we welcome it, we assume others will welcome it also. But I learned that when I took the exact same approach to some scientific statements that I would take in a room full of atheists, people got their feelings stepped on. I was met with emotional responses for doing something that would not have caused me to look twice. It was weird, and I finally just left the conversation.
So while we accept and encourage challenge to our ideas, without feeling hurt or scorned, I think some non-atheists feel a more emotional attachment to their ideas, so criticizing the idea is the same as criticizing them. I had come to accept this when it came to spiritual ideas, but then I saw the same dynamic when it came to scientific ideas. I have to admit, I was taken aback. Some were making 'points' but I saw it simply as a way to look more deeply into things that I may have misunderstood, or things that may have been presented in a misleading way, or something we could bounce around until we all came away a little stronger. That's not exactly how it went.
There is a different way of thinking, and I'm starting to understand that better now. I don't know if I'm able to engage it anymore, even if I understand it. It's like walking on eggshells when you can't just express criticism at an idea without a lot of drama following. So I've taken a mixed approach. For non-atheists that are as attached to their scientific ideas as they are their spiritual ideas, I need to just not engage. I won't get anything out of the discussion anyway---and maybe that is the result of a black and white view---and if it can be explained to others so that they understand that this is just how we discuss some subjects, and we don't take things personaly, then maybe I can have the conversation with them.
I've been backing out of a lot of conversations lately. They just reach the point where they aren't worth the effort.