I think the issue many christians have with atheist is the lack of respect they often show, the manner in which they often demean and mock the individual, it's insulting. They'll often carry themselves with an arrogance that's difficult to deal with - a persona of grandure due to their "enlightened" view of the world. No, not all atheist do this and I'm certain their are christians who are guilty of similar attitudes (atheist or christian or whatever else you're not free from being human). But you see the atheist mocking the christian constantly, the infuriating frustration the atheist often displays is difficult to deal with when it comes to having a simple conversation. Again, I'm not saying this is all atheist...I mentioned Penn Jillette in another post, a devout atheist who is one of the few who publicly handles this topic in a respectable way. He didn't always, at one time he was the epitome of what I'm describing here, but eventually he realized how ridiculous that was.

Just a side note, you could replace christianity with any religious view in my comments above. I simply used christianity as my basis because it's been brought up the most here and is generally the religion that is criticized the most by atheist, at least in western culture.