"Atheists like the Richard Dawkins of this world are just as fundamentalist as the people setting off bombs on the tube, the hardline settlers on the West Bank and the anti-gay bigots of the Church of England. Most of them would regard each other as destined to fry in hell.
"You have a triangle with fundamentalist secularists in one corner, fundamentalist faith people in another, and then the intelligent, thinking liberals of Anglicanism, Roman Catholicism, baptism, methodism, other faiths - and, indeed, thinking atheists - in the other corner." says Slee [the Dean of Southwark].
The people who bandy about these insults never seem to bother addressing Dawkins' standard response (HT B&W):
"Fundamentalist" usually means, "goes by the book." And so, a religious fundamentalist goes back to the fundamentals of The Bible or The Koran and says, "nothing can change." Of course, that's not the case with any scientist, and certainly not with me. So, I'm not a fundamentalist in that sense.
Similarly for accusations of "dogmatism". Almost any atheist will grant that their non-belief is provisional, and open to change if contrary evidence were to appear. Sadly, too many reporters and religious commentators seem incapable of distinguishing dogmatism from confident (but evidence-responsive) belief.
Note that one might have a very high degree of belief in some proposition, without thereby being at all dogmatic. I'm extremely confident that unicorns do not exist. But I'm not an "no-unicorns dogmatist", because new evidence could always change my mind. That's how rationality works. You align your degree of belief with your assessment of the evidence. The evidence (that I'm aware of) is stacked against gods and unicorns, so I don't believe in either. If my evidence changes, then so will my beliefs. Simple.
Probably what the critics are really meaning to get at is the idea that some atheists are outspoken and "evangelical", and hope to persuade others to their point of view. But isn't free inquiry and public debate a good thing? (Of course there are some contexts where criticising others' views would be inappropriate. But not all. There is a place for robust theological, no less than political, public debate.)
It's entirely possible for reasonable, "thinking atheists" to be strongly opposed to religion. Some may be opposed to religion because they think it is socially pernicious, propping up morally unjustifiable positions (e.g. anti-gay bigotry). Others may be principled evidentialists, and hold that one ought to believe what the evidence supports. They then oppose religion for the same reason they do astrology -- it's unsupported nonsense, and people are being unreasonable when they believe that stuff. Either basis for hostility seems perfectly reasonable to me.
At the end of the day, people who denounce "militant atheists" are promoting a double-standard, insulating religious beliefs from criticism when no-one would dream of offering other beliefs such protection. Over to Dawkins:
The world is made safe for people like [the 'God Hates Fags' crowd] and Osama Bin Laden because we've all been brainwashed to respect religious faith and not to criticize it with the same vigor we criticize political and other sorts of opinions that we disagree with.
If you can say, "such and such a view is part of my religion," everybody tiptoes away with great respect. "Oh, it's part of your religion," then of course, you must go ahead. In a way, we've been asking for trouble by moderate people persuading us to give to all religion a respect, which it has never done anything to deserve.