In the comments on Jerry's post I expressed one minor reservation about this open letter (or rather, agreed with one expressed by my good friend Chris Lawson). That aside, I endorse the letter. I share Jerry's sentiments, and I feel strongly about this issue.
Like Jerry, I'm especially sick of the attacks on forthright atheists by people associated with the NCSE. I'm also appalled at the spectacle of the NCSE cozying up to non-literalist theologians and fairly clearly suggesting that biblical literalism is not only false (of course it is) but theologically false (a body such as the NCSE should not be making theological judgments).
It seems that a lot of people associated with the NCSE have lost the plot. The aim is not to support a specific theological or philosophical position (whether it's atheism or some kind of non-literalist theism or biblical literalism). The NCSE may certainly want to cooperate in court proceedings with theists who dislike biblical literalism. Often it is necessary to litigate against government efforts to promote biblical literalism through distortion of the science curriculum. But cooperating with someone in court proceedings does not mean that you have to endorse their wider position out of court.
The point has been reached where the NCSE is adopting a substantive position in philosophy of religion (something like NOMA) and a substantive position on Christian theology (something to the effect that biblical literalism is theologically wrong). That goes beyond its remit. Or if it considers that part of its remit, it should say so openly. It then has to understand that many people who applaud its main efforts cannot give it their unequivocal support.
FWIW, I don't think it makes sense for someone who is not actually a Christian to say which Christian position is theologically correct. The Christian holy books, traditions, and teachings are open to many interpretations. It's not our business to say which interpretation of them is "right" as an interpretation.
I do, however, think that NOMA and similar positions are clearly false. Religion has never been confined to issues of morality and "meaning" in life or to describing a supernatural world that is hermetically sealed off from the natural one. Some modern-day religious positions may be that watered down, but much religion has made stronger claims about the interaction of a supernatural order of things with the world that we perceive with our senses. Indeed, that is far more typical of what religion has said over the centuries.
The NCSE should not be taking positions one way or the other on any of this philosophical and theological stuff ... not unless it wants to lose a lot of support. People associated with it should certainly not be wasting everyone's time and energy by attacking Richard Dawkins.