Here's what I keep wondering (a propos of all the discussion of the book Unscientific America, which continues at many blogs): what is it that people find so disturbing? I'm going to venture a diagnosis. Ultimately, it's the book's call for self-restraint. Mooney and Kirshenbaum's message to atheists is: please think about the consequences of being antagonistic. The mystery is that saying this unleashes such fury.
It doesn't seem to me that it is a bad thing at all to advise sensitivity to consequences. Take an example completely outside the realm of religion. Recently, Peter Singer has been writing and talking about rationing publicly funded health care: a few weeks ago in The New York Times, and now on CNN. His arguments are very reasonable, but folks are becoming hysterical right now about "death panels" and "socialism." In that setting, "rationing" is a dirty word. If Singer wants to help Obama achieve healthcare reform in the US (and he does) it would be perfectly reasonable to ask him to think about whether it's wise to speak out like this. I am pretty confident that Singer, and people who like Singer, would take no offense at this sort of strategic question being raised. (I don't know the answer--it's just the raising of the question that I'm defending.)
And so why is the same sort of discussion, when it comes to speaking about science and religion in the public square, so profoundly offensive to this book's very riled up atheist critics? I have a hypothesis: I think some of "the new atheists" feel like gay activists did in the 1960s and 70s. They feel like a vulnerable minority that's just now starting to be heard. Thus, it galls them no end to be told they need to tone it down and think about things that matter more--like science literacy, addressing the problems of climate change, etc.
I don't have anywhere near as strong a sense of atheists as muzzled and vulnerable. There are definitely issues about the status of non-believers and their right to be heard, but they don't loom as large in my mind as they do for this book's furious critics. The problems about the future--like climate change--loom much larger. If it's generally reasonable to think strategically about what we say in the public square, I can't see any reason to make an exception when the topic is science and religion.
This is not to side with Mooney and Kirshenbaum on any specific claims they make about who should or shouldn't speak out, when, and where, but just to say their views don't put them beyond the pale. Not even remotely. It takes a rather exaggerated notion of the plight of non-believers to find their call for self-restraint offensive.