Go read Open letter to the NCSE and BCSE. Or read it here:

Dear comrades:

Although we may diverge in our philosophies and actions toward religion, we share a common goal: the promulgation of good science education in Britain and America–indeed, throughout the world. Many of us, like myself and Richard Dawkins, spend a lot of time teaching evolution to the general public. There’s little doubt, in fact, that Dawkins is the preeminent teacher of evolution in the world. He has not only turned many people on to modern evolutionary biology, but has converted many evolution-deniers (most of them religious) to evolution-accepters.

Nevertheless, your employees, present and former, have chosen to spend much of their time battling not creationists, but evolutionists who happen to be atheists. This apparently comes from your idea that if evolutionists also espouse atheism, it will hurt the cause of science education and turn people away from evolution. I think this is misguided for several reasons, including a complete lack of evidence that your idea is true, but also your apparent failure to recognize that creationism is a symptom of religion (and not just fundamentalist religion), and will be with us until faith disappears. That is one reason–and, given the pernicious effect of religion, a minor one–for the fact that we choose to fight on both fronts.

The official policy of your organizations–certainly of the NCSE–is apparently to cozy up to religion. You have “faith projects,” you constantly tell us to shut up about religion, and you even espouse a kind of theology which claims that faith and science are compatible. Clearly you are going to continue with these activities, for you’ve done nothing to change them in the face of criticism. And your employees, past and present, will continue to heap invective on New Atheists and tar people like Richard Dawkins with undeserved opprobrium.

We will continue to answer the misguided attacks by people like Josh Rosenau, Roger Stanyard, and Nick Matzke so long as they keep mounting those attacks. I don’t expect them to abate, but I’d like your organizations to recognize this: you have lost many allies, including some prominent ones, in your attacks on atheism. And I doubt that those attacks have converted many Christians or Muslims to the cause of evolution. This is a shame, because we all recognize that the NCSE has done some great things in the past and, I hope, will–like the new BCSE–continue do great things in the future.

There is a double irony in this situation. First, your repeated and strong accusations that, by criticizing religion, atheists are alienating our pro-evolution allies (liberal Christians), has precisely the same alienating effect on your allies: scientists who are atheists. Second, your assertion that only you have the requisite communication skills to promote evolution is belied by the observation that you have, by your own ham-handed communications, alienated many people who are on the side of good science and evolution. You have lost your natural allies. And this is not just speculation, for those allies were us, and we’re telling you so.

Sincerely,
Jerry Coyne

Richard Dawkins has also commented on it.

I really feel that the NCSE has lost its way on this issue. I want to support the NCSE, but it has become increasingly hard to do. I have heard these arguments over and over again that they have to coddle religious believers because they need them to support science. They don’t. As we’ve said repeatedly, we aren’t asking that the NCSE give atheists even as much support as they do the religious: imagine if they had “atheist projects” or an “atheist coordinator”—there’d be rejection from the Christian community. We’re not stupid, and we know that the NCSE has a delicate political game to play as well, so all we ask is that the organization we’d like to support should be genuinely secular, and stay entirely out of the religion/atheism argument. It’s what they say they’re doing, but it’s not what they’re doing. And the hypocrisy is corrupting.

Nothing will change in what atheist scientists are doing. We will continue to support science and science education, but that doesn’t mean we will feel obligated to support the NCSE.

It’s funny. The organization has such a finely tuned political sense and diplomatic strategy to promote science to the whole of the United States, and have managed to profoundly alienate that segment of our society that is most dedicated to promoting science. That’s quite an accomplishment. Maybe we should stop supporting them because they’re that incompetent at the political side of their mission.