Reflecting on Cornwell's attack on Dawkins I am struck by something implicit in many of these attacks on 'militant' atheists. It is the suggestion that somehow the atheists are seeking to oppress the theists and even wipe them out. I think this is a fundamental misunderstanding of the atheists are trying to achieve.
As a conflict of ideas, clearly, at some level, I (and other atheists, including Dawkins) would like to persuade theists to be atheists. But this is very much in the same way that I would like people to agree with me on every other topic. But you don't see Tories, Evolutionary Psychologists, soap watchers, Hip Hop fans, or dualists protesting that I seek to wipe them out just because I disagree with them. If theists are arguing that just by disagreeing with them atheists are seeking to oppress them they are quite fundamentally, and comically, wrong. Even when leftists argue that George Bush and his neoconservative coterie have blood on their hands - this is not taken by right-wingers in general as the prelude to some latter day Holocaust. Indeed I happily tolerate the right of theists to have their own protected space in newspapers to attack us atheists, or for the Chief Rabbi (here, 38mins in), or Archbishop of Canterbury to try and convert me to their way of thinking.
But I don't think that is the sense in which most theists feel they are being oppressed. Atheists also make some political demands that some of the privileges religious groups receive be revoked. In particular, atheists are rather unhappy about state funded and delivered religious indoctrination (such as 'Faith Schools'). They are also quite unhappy about the second chamber of the legislature being populated by Anglican bishops. Looking at the National Secular Society or British Humanist Association you can see they have also campaigned on topics such as Catholic adoption agencies seeking to discriminate on sexual orientation while still receiving government funding, or legislation seeking to outlaw religious 'hatred'*. All these topics are challenges to religious believers - but they are challenges to the special status that they are granted in society, to particular exceptions to the normal way we go about doing things just for them. To characterise this as oppression shows just how religious believers have had things their own way for too long.
*Note that I object to this particular law and the way it was drafted, I'm broadly sympathetic to attempts to oppose religious hatred as an ethnic marker (i.e. the BNP and Muslims).