For the most part, I couldn't help but agree with everything he said. For the most part.
The first three-quarters of the book is written by Miller the molecular biologist. He attacks with scientific rigor and reason the "anti-scientific" positions which many religious people argue (or, at least, their vocal proponents argue): God as charlatan (pure creationism), God as magician (intelligent design), and God as mechanic (deism). Examples abound. Scientific experiments are explained in accessible terms. There are even diagrams.
Miller also quite eloquently explains, as he debunks these unscientific "theories," why basing a theology on any portion of scientific understanding is a dangerous game. The Victorians, who believed the universe ran as a great mechanistic machine, found themselves trapped in a deism that couldn't handle the scientific discoveries of quantum mechanics. The proponents of intelligent design, in pointing to supposedly "irreducibly complex" systems and claiming the handiwork of God, lose spiritual ground every time one of those systems is explained scientifically. One's religion and one's science should be separated, because science is always making progress; that progress should not be resisted because we have placed our religion within the gaps in the current scientific framework.
He then turns his criticism (and rightly so, I think) toward the "militant atheists," those within the scientific community all too willing to dress their own personal opinions with the cloak of scientific authority. He expounds upon what evolution tells us and what it does not; he explains that evolution, and science, do not have to be based upon a philosophical materialism in order to be believed or trusted. Miller does an excellent job of explaining that this use of evolution as a weapon against religious belief (cf Dennett, Dawkins, Wilson, Lewontin, etc) is likely what causes the ordinary person to resist evolution as an idea. We need our lives to have meaning; it is not science's place to say whether or not our lives actually do have meaning. But when the fierce proponents of materialism use science to bludgeon purpose and virtue, ordinary folks will obviously react to science negatively. The entire "debate" hurts both sides.
But after all of this positive work, Miller explains that he still believes in God, not only because God and science can be separate, but also because the science of quantum indeterminacy and random mutation gives God a way to interact with our world.
So in the end, Miller has done precisely what he warned against doing - using current scientific understanding, which is always subject to change, as validation of his particular theology.
I can't say that I totally disagree with his assessment. I myself find the inherent indeterminacy of quantum mechanics to be a tremendously beautiful - spiritual, even - system, within which anything and everything has its chance to become reality. But I will not balance my spiritual belief upon the knife-edged fact of quantum mechanics being true. It's as true as we know anything to be, sure. In that sense, it's a scientific theory which is more valid than those which preceded it, and so I will argue that a philosophy based on quantum mechanics is more valid than one based on a scientific theory which has since been disproven. But that's not quite the same as building up a philosophy/theology from a scientific theory.
In the end, I mainly agree with Miller simply because I believe in what he's trying to do. I believe that science is not self-sufficient as a philosophy of life, and I believe that religion (spirituality) is not meant to explain the nature of the universe. When you behold a piece of art, knowing how it was technically constructed, or knowing that it is religious in nature, is each not enough to appreciate it. That greater human passion - wonder - lies at the heart of both the scientific and religious drives, and we are not whole without encompassing within ourselves both our reason as well as our emotion.
As Darwin himself said in the closing sentence of Origin:
There is grandeur in this view of life; with its several powers having been originally breathed by the Creator into a few forms or into one; and that, whilst this planet has gone cycling on according to the fixed law of gravity, from so simple a beginning endless forms most wonderful and most beautiful have been, and are being evolved.