Eliezer, The claim isn't that you should not hate religion. The claim is that sociologically, this post is a bit like giving the Hated Enemy a kick in the pants. The point in it is fairly obvious (though, as people point out with the chronology, possibly historically false). People who already want to laugh at religion get to go "har-har", and people who for whatever reason want to not laugh at religion get to feel alienated from whatever it is you're up to here.
It is one of those posts that makes me wonder more acutely what you are up to here. Some months ago I found your writings on the singularity, seriously considered giving the SIAI money, and instead spent a great chunk of time trying to launch a disaster-averting effort of my own. I am still devoting most of my divert-able time toward launching that project because I still think (partly on the basis of your arguments) that reducing existential risks is the most important thing most of us can accomplish. Do you? Is this blog a way to recharge so you can return to the work at hand? Are posts like this somehow part of the research you are doing on Friendliness? Is explaining to people how Christianity could look foolish (via posts like this, which aren't even especially well done or anything) a separate good as worthy of your time as whatever work it displaces? Am I missing a possibility here?
As to whether today's readers want a 500 page tomb:
I haven't done a study, and I'm sure there are other examples. But the two books I can think of that drew large numbers of excellent students to do research with the authors are Douglas Hofstadter's "Godel, Escher, Bach" and Allan Bloom's "The Closing of the American Mind". Both are surprisingly difficult to read.