I think, if Dawkins is annoyed (and I am prepared to consider the evidence and decide in favour of his being so), that it is because he has been banging on about this for 30 years and getting the same old misunderstandings and misrepresentations in response.
He is not trying to "convert" anyone to atheism, as atheism is not a religion and therefore does not seek converts. What he is trying to do is to get people to THINK. To question their beliefs rather than accepting blind faith. To apply the same rigorous criteria to claims of faith as one would to claims of science - evidence, method, results, conclusions. I don't think that's unfair, or militant, or fundamentalist, or anything else he has been accused of being.
I agree he isn't the fluffiest of debaters, but people shouldn't mistake sharpness of tone for arrogance in the actual content.
As for herbal remedies, either it works in independent clinical trials, in which case it's just "medicine", rather than "alternative medicine" - or it doesn't, in which case it's charlatanism. That's the only test needed.
On the morals/faith thing - having morals outside a religious framework is more than a matter of faith that what you are doing is right or wrong. It's all about seeing them in action. You treat people the way you would be expected to be treated yourself - that's the basis of it. So you don't steal, because you wouldn't want to be stolen from. It's not perfect, but neither is Christian morality.