While I am all for communal bathrooms, I think the issue is mostly the physical components and peoples feelings about them. Let's say you are forgetful or just plain lazy and don't lock the stall door to ensure your privacy. Someone opens the stall door assuming no one is in there and runs into you on the toilet. It is much less embarrassing to be caught with your pants down by someone of your own gender rather than someone with different plumbing "down there" than you have.
Plus there's the rumor that men are more dirty and unsanitary than women so women would be less inclined to sit on a toilet that recently had a dirty man's behind on it.
