I've seen several atheists here talk about Zeitgeist here in a positive way. By Zeitgeist I mean the movie, not the general term for "spirit of the ages." Zeitgeist is not a friend to atheists, or anyone else. Yes the first section is about religion and from a skeptical point of view, but they substitute supposition for fact in the same manner that they do for the sections on 9/11 being an inside job and the banking system being a world wide conspiracy. I'm no friend to religion or capitalism, but I know to rely on facts instead of conspiracies and pseudo scientific attempts at debunking. See the wiki article for more details.
And regardless of whatever good intentions they may have or things they may say it's a mistake to get in bed with truthers just because they don't believe in a god.