Hmmmm. I think there are a couple issues here. One is, people adhere to their beliefs becuase, by default, they believe their beliefs are the most correct or right for them. Logic leads the rest of that thought to be that beliefs outside of that are incorrect or not right or...dare I say...wrong.
Now, believing your beliefs are right and others are wrong does NOT mean you believe others are BAD or IGNORANT.
I, personally, have a whole set of reasons I believe there is no god (to oversimplify my beliefs entirely) and when I see people who believe otherwise, clearly I don't agree with their conclusion. I think they are wrong. I do NOT think they are bad or ignorant.
By the same token, when I was in about second grade I remember getting into a debate with another kid about multiplying negatives (yeahhh I was a bit geeky). The other kid was ADAMANT that you couldn't do such a thing because if it's already a negative/less than zero, then how can you have 'many sets' of 'less than zero'. I *knew* you could multiply negative numbers. It's a fact. But the other kid just hadn't gotten to that point yet. He was wrong. I was right. It doesn't make him an idiot, or bad, or ignorant. In fact, he was in the same program I was in for highly gifted kids, which clearly means he's 'got what it takes' to comprehend higher level math at some point. He just hadn't gotten there yet.
Now, if I had made fun of him or called him stupid (which, being in second grade, is entirely possible LOL) that would be inappropriate. So to translate that to religious beliefs, it's not ok to make fun of or insult people who believe differently. But there can only be one answer. There either is god, or their isnt. So either the people who don't believe in god are wrong, or the people who do believe in god are wrong. It can't work both ways.
I'm going to pick on HennyPenny for a sec because I know she'll take it the right way (

ya HP!) and understand the point I'm illustrating without taking it personally. I consider HennyPenny to be an extremely intelligent, compassionate, well read person, and I've learned a lot from her. We can agree with each other probably 90% of the time on MDC, and she's one of a short list of online folk I'd love to hang out with sometime. However...she believes deeply that there is a god. I don't. She disagrees with me. I disagree with her. We've even had some pretty deep debates about it. I do NOT think she's ignorant (far from it), and I'd wager to say she feels the same about me. But one of us is wrong (not bad, stupid, idiotic, or anything else, just incorrect). I don't think it's me, she doesn't think it's her. But by default, someone is. When we're discussing the validity of atheism vs. theism there can only be one correct answer. I'm not saying we can prove either belief without doubt, but suffice it to say each camp believes they are right and can 'back up' their claims.
Just because we're talking religious concepts instead of math concepts means it's a more emotionally loaded issue, not that it negates the use of logical process.