I actually originally wrote the following post as a comment on this post at PZ Myers' blog pharyngula, but I decided to repost it here too:
I think there is one issue relating to the non-destructive elements of religion that is all but ignored by the new atheists, namely the belief in a non-supernatural (read natural) God of the sort espoused by Einstein, Spinoza and many many other scientists, empiricists and science-minded lay people. These believers think that the conception of God adds something to their understanding of the universe, even if, at its core, the concept is mainly metaphorical or poetic. There are several different concepts of God which are perfectly compatible with the naturalistic world view.
It seems to me that the real "enemy" is supernaturalism or even faulty/poorly maintained/poorly constructed belief generating mechanisms. You're not gonna find any non-realists on God or pantheists flying planes into buildings, trying to teach your children fairy tales as science, or insisting on the divine authority of scripture. Yet even Einstein, one of the best minds man has ever produced found his understanding of the universe incomplete without some concept of God.
So long as there are believers in the supernatural the naturalism/supernaturalism debate may take precedence over the debate over whether room should be made within the naturalistic world-view for the explanatory frame-work of a natural conception of God, but this will have to be addressed. And it is my belief that without the need to defend against God's supernatural implications many self-styled atheists may find that the addition of a natural God does add something valuable to their world view, even if that value is mainly in God's symbolism, metaphor or poetry.