Sam Harris recently posted Atheism’s Wrong Turn, an article by Damon Linker in The New Republic. I don't want to address the entire thing, but at least part of the premise it's built upon. As Linker puts it:
That’s because “the new atheism” is not particularly new. It belongs to an intellectual genealogy stretching back hundreds of years, to a moment when atheist thought split into two traditions: one primarily concerned with the dispassionate pursuit of truth, the other driven by a visceral contempt for the personal faith of others.
Today’s bellicose atheists are part of the second tradition.