The rest of chapter 8
Scientists as a group are more secular than ‘the rest of the nation.’ Religion is an emotional matter. Creationists fear that evolution [the subject, not evolution itself] will ‘undermine their religious culture.’
Abrasive atheism can only exacerbate this anxiety and reinforce the misimpression that scientific inquiry leads inevitably to the erosion of religion and values. [p. 100]
They apparently mean ‘abrasive atheism’ of scientists there, but they failed to specify that, which is one problem throughout – a constant tendency to overbroaden their claims and confuse the issue. As it stands the claim is nonsensical – ‘abrasive’ atheism as such can only exacerbate fear of evolution? Well, possibly, but it’s not obvious how CM and SK know that. In any case what would one be expected to conclude from that? Abrasive atheism in general will have X predicted bad consequence, so…what? Everybody everywhere should stop being an abrasive atheist? That would be asking a lot.
But they do ask a lot. That’s the problem.
To further the cause of scientific literacy, we need a different, and far more sympathetic, approach, one that’s deeply sensitive to the millions of religious believers among our citizenry. [p 100]
See what I mean? That’s asking a lot. It’s asking a great deal too much. We’ve had that – we’ve had years and years of nearly everyone being deeply sensitive to the millions of religious believers among our citizenry, and we don’t want to be deeply sensitive any more. We want to talk freely. The millions of religious believer can toughen up a little and get used to disagreement.
Then there are two pages of fundamentally irrelevant stuff about history, which demonstrate only what we already know, that people can combine incompatible beliefs, and have done so in the past. Then we get back to the advice.
The official position of the National Academy of Sciences and the American Association for the Advancement of Science is that faith and science are perfectly compatible. It is not only the most tolerant but also the most intellectually responsible position for scientists to take in light of the complexities of history and world religion. 
That hasn’t been demonstrated.
The problem with the New Atheism [sic], however, isn’t just that it’s divisive or historically incorrect about the relationship between science and religion. It’s also misguided about the nature of science. 
Then there are a couple of pages on the putative distinction between methodological naturalism and philosophical naturalism, which is treated as if it were gospel.
The American scientific community gains nothing from the condescending rhetoric of the New Atheists [sic] – and neither does the stature of science in our culture. We should instead adopt a stance of respect toward those who hold their faith dear, and a sense of humility based on the knowledge that although science can explain a great deal about the way our world functions, the question of God’s existence lies outside its expertise. 
And that’s about it. I’m not skipping the part where they present a real argument, because there isn’t one. There is some handwaving about methodological naturalism versus philosophical naturalism, but nothing we haven’t seen on their blog.
One thing that’s interesting about this is that it shoots to pieces Mooney’s recent claims that he hasn’t been telling anyone to shut up. The whole chapter is all about telling ‘the New Atheists’ to shut up – not literally as in ‘Hey, New Atheists: shut up!’; but plainly nevertheless, as in ‘We should instead adopt a stance of respect toward those who hold their faith dear.’ It’s true that it’s not literal censorship, or even a literal command to self-censor – but it’s pretty damn close to being the latter. It is very strong moral advice to self-censor. I think it’s pretty disingenuous of Mooney to keep expressing shock-horror that everyone thinks he’s telling us to shut up. That is pretty much what he is telling us.