Michael Ruse, who is an atheist, argues in favor of tolerance and respect for people of faith in an excellent column that criticizes the militancy of the "new atheists", which he posted at the Guardian website. He lays out four broad reasons why he disagrees with them, and I think anyone interested in this topic will find that it makes for great reading.
I thought the following comment that he wrote in that column about the reaction he has gotten from some of the militant atheists was rather telling:
I am not whining (in fact I am rather proud) when I point out that a rather loud group of my fellow atheists, generally today known as the "new atheists", loathe and detest my thinking. Richard Dawkins has likened me to the pusillanimous appeaser at Munich, Neville Chamberlain. Jerry Coyne, author of Why Evolution is True, says (echoing Orwell) that only someone with pretensions to the intelligentsia could believe the silly things I believe. And energetic blogger PZ Myers refers to me as a "clueless gobshite" because I confessed to seeing why true believers might find the Kentucky Creationist Museum convincing. I will spare you what my fellow philosopher Dan Dennett has to say about me.When Dawkins, Coyne, and Myers use such vitriol against a fellow atheist who doesn't toe their particular party line, this shows that their brutish behavior is not directed only against people of faith, but against anyone who thinks differently from the way they do.
I especially appreciated his comment about how tactically foolish it is for those who want to promote the teaching of evolution in schools to attack religious people who otherwise might be your erstwhile allies. This is in contrast to PZ Myers, who wrote a few years ago that he opposed efforts like the "Evolution Weekend" project that many churches promoted, because it would mean allying himself in some sense with some of the very people of faith he was busily insulting.
It is a remarkable idea that atheists and people of faith might actually be able to get along. The fundamentalists of both the atheist and the religious camps can have at each other. The rest of us, Michael Ruse included, can try to find a common ground for dialogue and move forward.