Do you get out much? Honestly as a guy I'd never want to sit down in a men's public restroom (unless it is an extremely well kept place).
That's not to say any public restrooms are generally good, but the idea that women are somehow cleaner than men really needs to die.
The assumption I've always been given is that women are more prone to hovering (germs!) along with the obvious biological differences that allow for more..erm...variety in terms of mess making. Seemed a sensible enough explanation to me, but it's very possible that there's more to it.
Another note, I remember reading somewhere that the amount of bacteria found in bathrooms is much higher in ladies-rooms than mensrooms. May or may not be the result of overall messiness, though :-)