My understanding is that the "women only" cars in Tokyo are not strictly enforced. If a man boards such a car during the morning rush hour, the worst that will happen to him is a scolding from the irate women around him. It's sort of like the "turn off your phone in the priority seats" rule.

If there's any way to stop the molesting problems that have plagued Japan's commuter trains, it's more assertive responses from the women. This is a shame-based society we're talking about, and publicly shaming the men who are groping women on the trains is a very effective way to make them stop. In fact, this seems to be on the rise nowadays: women aren't taking this behavior silently any more (at least not as often), which is definitely a good thing. Seems to be a much more effective solution than sticking people in separate cars.

I do like the common Japanese policy of seating single female passengers together on overnight buses and other long-distance transportation... a much more tailored way to prevent unwelcome altercations.