Disney bathrooms tend to be much cleaner than regular public bathrooms. The larger ones seem to be cleaner than the smaller ones. So the one by the Tomorrowland Noodle Terrace that has only 3 stalls, was not as clean as the larger ones. I must say, that the last time I was there 3 weeks ago, there was a line out the door for that one, and there was an attendant there cleaning it while I was there. There is just so much you can do in a tight space.
On the other hand, most of the bathrooms are huge, and my favorite in Hollywood Studios is by Light Motors Action, is so big, it is very clean and you never have a wait.
Of all the bathrooms I visited, it was rare not to see an attendant cleaning it. Those people really work hard and Disney understands that keeping bathrooms clean is a priority for guests.