If you haven't heard, Pope Benedict mentioned in a speech to Queen Elizabeth that he felt the Church was threatened by "secular extremists" and thought that atheists are no better than Nazis.
(we'll just get this out of the way now: what was Benedict's summer job, again? Oh right, the Hitler Youth... And what faith were most Nazis, including Hitler? Roman Catholic... And what did the Catholic Church do during Hitler's reign? Oh yeah, pray for its success...)
Now look, I might as well say what's been on my mind for some time: GODWIN'S LAW IS OVERRATED. It's well intended, but the fact is that if you've been out in the real world you know that there are a lot of people out there who think that everyone who isn't the same nationality, skin colour, religion, or sexual orientation as themselves should be wiped out. That's not an exaggeration or "liberal bias", it's the truth -- ever heard of the Aryan Brotherhood (or anything coming out of Ann Coulter's mouth)? Heck, if you've seen my video or blog on the Qu'ran burning campaign started in the United States, you'd know that there's some disturbing parallels to the Third Reich becoming more and more common in American conservatives.
Anyway, to directly address The Pope's point... There are definitely extremists in every belief system -- and for all intents and purposes, that includes Atheism -- but to say that every Atheist is an extremist is utterly untrue and disingenuous (great, another clergyman who can't follow Jesus' teachings to save his life...). In my experience, most Atheists just want organized religion to butt out of the government, and to leave them alone personally.
If anyone in any belief system deserves to be compared the Nazis, it's the fanatics (and possibly the fundamentalists) that appear in nearly EVERY religion (the most obvious evidence of that are groups like Al Qaeda and the Westboro Baptist Church). Then again, acknowledging that would need The Pope to acknowledge that Mother Church is fallible (which goes against ecumenical policy), and it would arguably require saying that The Pope's most devoted followers could be a problem. So yeah, I'm not holding my breath.
Look, is it really too much to ask that the leader of the largest religion in the world, actually try to teach his followers to be PEACEFUL instead of thinking everyone's out to get them? With an attitude like that, it's only going to be a self-fulfilling prophecy.