The real reason I find myself vaguely defending some religious ideas against village-atheism is the same reason I used to go around getting into arguments with libertarians. It's that overly simple belief systems really annoy me, even if (especially if) I mostly agree with them. Libertarians used to make me crazy, because I always knew exactly what they would say in any situation (the spur for this post is this column (TNR subscribtion required) which makes the same observation about the New York Times op-ed libertarian, John Tierney). Same for the atheists, like PZ Myers. I can pretty much predict his reaction to any piece of news involving religion, which makes his posts on those subjects information-free (they can be entertainingly nasty though).
I guess I don't like fundamentalisms of any sort. Libertarianism and atheism both tend to be all-explanatory and ignorant of nuance. Libertarianism in its fascination with the distributed market model ignores anything which doesn't fit its framework, such as public goods, distortion of the market by the overly powerful (who can manipulate it unfairly) and the poor (who may have no motivation to respect property rights). Atheism tends to ignore the nature of religious belief, treating as something like bad science, rather than trying to understand what it might really be about. Let's just say God is the referent of the word "God", and while it may not exist the way a chair exists, it has a real conceptual role in thought which it might be useful to understand.