Unfortunately, even those who are generally sympathetic towards atheists tend to harbor various misconceptions and biases. A recent post on one of the Atlantic blogs is a good example. Ta-Nehisi Coates post, "The Most Effective Argument for Atheism That I've Ever Seen" is not outright hostile, at least in comparison to what others have written, but it is laced with myths and ignorance. He characterizes atheists as fundamentalists and as being angry. He also makes it pretty obvious that he knows very little about atheists/atheism. The argument he refers to is not a bad one but it is by no means the most effective.
It is also interesting that he ends his short post by stating, "If you can't talk without driving into the margins, or insulting someone, try not talking. You don't have to speak on everything." It never seems to occur to Coates that perpetuating myths and misconceptions is insulting. The last sentence seems design to insulate himself from criticism. Personally, I think if you are willing to comment publicly then you should not only be open to criticism you should encourage it. Just try to make sure any critical comments are actually supported by reality.