Now that you mention it, this is true among people who I know as well. I don't know why that might be and I don't particularly feel qualified to theorize about it. It's definitely strange. Murakami's women have always struck me as very female-as-baffling-other-as-seen-by-self-absorbed-straight-male, especially in Sputnik Sweetheart, which one might think wouldn't have this problem but which, if it was intended not to, backfired horribly.
I haven't read Murakami myself, but I also know many women who love his books. Could the answer be that Murakami actually understands women better than you think (or, understand them better than you do?)? Obviously, that may be totally wrong - and not having read his books I can't tell - but I kind of doubt that a writer with such a poor understanding of women could have such a large female fan base.