OK, let's not blow this totally out of proportion. The unspeakable evil here is the usual operating conditions of your average MTA restroom, which is not fit for use by man, woman, or anything in between.
Having said that, I don't get what the brouhaha is about. No rational person should believe there is any real safety in a public restroom in a NYC subway station. Whether the other occupants of the restroom are genetic or wanna-be females, you need to keep a close watch on your person and belongings. Remember, this isn't the restroom at your central-Kansas family restaurant where you chat with your girlfriends about, as one previous post mentioned, "female problems". This is a vile disgusting facility where no respectable woman should be spending time, anyway. I'm not sure if anyone who wants to use these restrooms should be rewarded for their bravery or condemned for their stupidity, but worrying about which room someone is going in is irrelevant.
The difference here is that in this case the restroom has been intentionally made even less safe by a dictate of city policy and law. This is a HUGE departure from the previous status quo of the area being unsafe but allowing people forced into using them some degree of recourse if they should be harassed or victimized.
I think that what most people are objecting to in this matter is a needless coarsening of an already coarse culture. Rather than making public facilities safer and better so that you don't HAVE to know all of the nearby restrooms in department and bookstores as other posters have mentioned, the MTA has bent to political pressure and fashion and made it so that these places are now a safe place for perverts only, and anyone who dares to object has no legal standing whatsoever.
I don't think that this ruling makes New York City a nicer, cleaner, safer, or friendlier place; quite the contrary. It's an additional lowering of long-accepted standards and a further flight from normalcy as a result of a spineless retreat from the shrill voices of political correctness.