I would love to be able to just ignore the fringe, the rude people, the fanatics, I feel that I need to address them, even if briefly, because they are the most visible element of both factions. Some people are just assholes. It doesn't matter if they are Christian, Muslim, atheist or Buddhist. When those people start hanging around together, they feed each other's fire. Add to that the convenience and relative anonymity (facelessness, anyway) of the internet, and the outcome is completely predictable. Those people are not helpful, but can be, I think, safely ignored.
For the rest, it gets tricky. I am certainly not one of those people who thinks that atheists should shut up about religion. For one thing, the subject is absolutely fascinating. I enjoy discussing religion. I even enjoy having the same conversation again and again. I find that many theists are unfamiliar with what atheists have to say, and are often genuinely curious about our position. I don't mind going around the ring with them, refuting the same tired arguments again and again. I don't really get upset with Pascal's Wager because I know that, for a theist, it is a genuine question. This is why I have a blog - I really enjoy the conversation.
Beyond the fun, however, I believe that the conversation is important. It is important precisely because of the angry fringe that we would all love to ignore. If there weren't angry asshole atheists, then the calm, middle of the bell curve theists wouldn't think that atheists were terrible. And if there weren't angry asshole theists, promoting mythology instead of science, fear instead of reason and bigotry instead of fairness, atheists wouldn't have much to complain about either. In the communal conversation that I, as a member of the atheist community have with the rest of the world, it is absolutely imperative to remember that most theists are not jerks. They are not my target. It is true that I think that their beliefs are poorly-founded. I think that they are deceived and deluded. I know that their superstition is causing a lot of other people grief. And yet they are nice people. We can have perfectly wonderful conversations without a single mention of the issues that set all of us off: healthcare, same-sex marriage, evolution. I have to force myself, on occasion, to willfully ignore some element of someone's life that would preclude friendship. I have written about that here, in fact - I have a hard time taking Republicans seriously. As a resident of North Carolina, I am sure I deal daily with Republicans and theists, and yet I manage to get through each day without a single argument or angry word.
One further thing to consider is that an ugly conversation never changes anyone's mind. In the podcast I mentioned above, the atheist-turned-theist's reason for change was not based on any kind of reason whatsoever. That is not an insult - he says this in so many words. His conversion was a purely emotional (he would say divinely-inspired) response. This is what makes the religion debate so very frustrating: neither side is willing to give a single inch, and that is because we aren't really arguing in the same reality. We are like people playing laser tag in a hall of mirrors - we can interact with each other, but we are approaching the debate from completely different planes of reality.