Atheists who choose to argue the existence of gods with the religious will often be accused of being rude, intolerant, bigoted, close-minded and arrogant for having the nerve to say, "I don't think your god exists and here is why."
What will usually happen eventually, is that the atheist will say, "Your argument is stupid!" in a fit of frustration, or, "Your beliefs are stupid!" Here is where dialog breaks down and both sides stomp off. Where is the disconnect? Contentious dialog is difficult, even for those experienced in it, but why does dialog stop once ones ideas or beliefs are attacked?
Atheists, even the most outspoken, are usually very careful to separate the individual from ideas and beliefs. "You're a Christian and Christianity will cause you to have stupid beliefs," is technically different from, "You're a Christian and you're stupid." However, I don't think it's understood differently from the Christian perspective.
There certainly are atheists who think anyone with a belief in a deity or deities is stupid. There are others who hold this same viewpoint who will hide behind the language provided earlier in an attempt to appear fair-minded and open to dialog. My hope is that those who hold bigoted viewpoints would simply state them without trying to play games with language.
Ideas and beliefs don't need protection, people do. I think as long as people define who they are by what they believe, questioning an individual's beliefs will always be inferred as a personal attack which degrades dialog. To me, saying, "I don't think YOU'RE stupid, I think the beliefs you hold are." is similar to saying, "I don't hate you because you're gay. I hate the gay sex you have."
I don't think that religious belief should be free from criticism. I think that much progress can be made in dialog if both parties can agree that beliefs are different then who we are as individuals. From the religious side, when an atheist says, "I think Jesus rising from the dead is a stupid belief," they mean the same thing you'd say to a Scientologist, "I think that the idea of thetans is stupid."
It is difficult to resist an emotional reaction when the ideas and beliefs you hold are challenged, but that is the only way to have a reasonable dialog with someone who disagrees with you.