Dawkins doesn't bother me any more than any other atheist I've read. The fact that he lives and is popular in my time makes him no more threatening to my faith than Thomas Paine, Voltaire, Lucretius, A.J. Ayer or Bertrand Russell. I know where my faith fits in the history of ideas, and I'm comfortable in the capacious intellectual house it affords me. Dawkins is amusing at best, annoying at worst. As a philosophical atheistic thinker I find he's small beer indeed and I'd rather read Nietzsche.
In my own intellectual journey (not necessarily the same as my journey of faith), I find no attraction to reductionism of any kind. It's always seemed to me a truncated worldview, artificial and strained, ignoring the real content of our deepest intuitions of meaning, beauty, love and justice. I side with Plato and Cicero contra Lucretius, Aquinas contra Bacon, etc. (yes, Bacon was a Christian, I disagree with his metaphysics). I believe the Scientific Revolution was a necessary reform on the excesses of Aristotelian Physics, but in many ways we through the baby out with the bathwater when we chucked Formal and Final causes out by fiat. But that's another discussion...
I write that preface to provide some context on what my real concern is with regards to Dawkins and the legions of young enthusiastic atheists that I run into, in person and on the web: the absolute philosophical illiteracy of so many naively confident advocates of reductionist science and the silly caricatures of faith they hold to. Mostly what I find in this generation of non-believer is not reflective, self-conscious atheism but rather an inherited, brittle and angry atheism that assumes the final triumph of reductionist materialist science has been accomplished. For these dogmatics the mere existence of faith or religion of any kind is really appalling and a cause for anger and aggression. There's simply no difference between, say, Wendell Berry and Pat Robertson, C.S. Lewis and Jerry Falwell, Dostoevsky and Fred Phelps.
It's just flat strange and saddening to me, to know that there are those who truly think that the Santa Clause analogy would have been devastating to St. Augustine or Tolstoy or Tolkien. That the existence of reflective intellectual Christians like Annie Dilliard, Flannery O' Connor or Walker Percy so long after Darwin is merely an anomaly to be ignored.
This kind of naivety makes not only for fruitless engagement across the theistic/atheistic boundaries, but for increasing hostility and social disintegration. When I read Dawkins and those that find his simplistic reductions of religion intellectually appealing, I'm not offended as a believer, I'm not threatened intellectually, but I am discouraged about the future of community. If the main participants in the the great God Debate (which is really no more acute now than at any other time in history, and probably a good bit less than late 19th Century Britain at least) don't have the intellectual resources or emotional charity required for deep engagement of such a weighty matter, then we not only have more anger, hostility and misunderstanding, but we become more impoverished in our self-understanding on both sides.