Are some atheists too aggressive?
(I think the distinction between tolerance and respect is a very important one, by the way. We owe tolerance to pretty much everyone and everything unless they produce effects or behavior which are obviously intolerable. Respect, with its connotation of approval and admiration, is a very different matter and needs to be earned.)
Nevertheless, we manage to deal with people who believe all kinds of nonsense (astrology, flying saucers, psychic powers, crystal healing, and what have you) and even interact pleasantly with them, precisely because people tend to avoid confronting each other about such matters. The same goes for people with differing political opinions. A person who insists on getting confrontational about such differences at every opportunity quickly develops a reputation as a social boor and is avoided by everyone, regardless of the objective merits of his own views.
I don't agree with those who are criticizing Dawkins and Harris themselves. We need Dawkins and Harris. They're advocates for the plain and simple truth. As I've pointed out before, there's no reason why all atheists should have the same agenda or tactics or have anything in common at all -- any more than all people who disbelieve in unicorns have anything in common.
To me, it comes down to the circumstances. On this website, I'm completely straightforward about what I think. If some people find this disagreeable or inappropriate, they are free to find something else to read which is more to their liking. In ordinary social or work situations I generally avoid discussing de facto controversial subjects unless the other person invites it in some way. And as for moderate, secular Christians (or other religious people) who are as supportive of the separation of church and state as we are, cooperation with them is a pragmatic necessity in the cause of resisting the fundamentalists as effectively as possible (see here, and the last paragraph of this). One must agree to disagree about differences, for the sake of the common interest.