Andrew Sullivan picks Coyne's the money quote:
[S]ome theologians with a deistic bent seem to think that they speak for all the faithful. These were the critics who denounced Dawkins and his colleagues for not grappling with every subtle theological argument for the existence of God, for not steeping themselves in the complex history of theology. Dawkins in particular was attacked for writing The God Delusion as a "middlebrow" book. But that misses the point. He did indeed produce a middlebrow book, but precisely because he was discussing religion as it is lived and practiced by real people. The reason that many liberal theologians see religion and evolution as harmonious is that they espouse a theology not only alien but unrecognizable as religion to most Americans.
Jeff Coyne is correct in stating that Richard Dawkins and other New Athiests write "middle-brow" books because of the common, uncultured religion (if you see Bill Maher's movie Religulous you'll see what sort of religious people are really the target). But those who argue on behalf of a more cultured, philosophical, "high-brow" religion are not arguing in vain. You see, if Dawkins was targeting only fundamentalists, or only the ignorant religious, or only a specific segment of religion, then Coyne's objection would be an adequate defense.
But in my readings of Dawkins (this is actually more true of Hitchens but still seems true of Dawkins) it seems to me that for Dawkins, religion is inherently destructive; that religion is always delusional, that it always fosters hatred and dischord. And if they are trying to argue that all religion is damaging, hateful, etc., then they will have to come to grips with the fact that there are some very smart, reasoned, subtle, liberal traditions of religion as well. Otherwise, what Dawkins is arguing against when he targets religion and religious education is not stupidity, closemindedness, and bigotry inherent in religion, but stupidity, closemindedness, and bigotry that is attached to religion by the human beings who interpret it. The same stupidity, closemindedness, and bigotry that can manifest itself in nationalism (again: Obama's nationalism is not the same as Bush's nationalism) or even economic theory (as Communism/Capitalism proved).
Either Dawkins is targeting religion as a whole, and therefore needs to defend his argument against the intellectual elite of religion, or else he is only targeting ignorant religion, and therefore the burden of proof lies on him to prove that it is religion, and not ignorance.
(I'll quote it again, from Albert Camus:)
The narrator is inclined to think that by attributing overimportance to the praiseworthy actions one may, by implication, be paying indirect but potent homage to the worse side of human nature. For this attitude implies that such actions shine out as rare exceptions, while callousness and apathy and the general rule. The narrator does not share this view. The evil that is in the world always comes of ignorance, and good intentions may do as much harm as malevolence, if they lack understanding. On the whole, men are more good than bad; that, however, isn't the real point. But they are more or less ignorant, and it is this that we call vice or virtue; the most incorrigible vice being that of an ignorance that fancies it knows everything and therefore claims for itself the right to kill. The soul of the murderer is blind; and there can be no true goodness nor true love without the utmost clearsightedness.