I've actually asked such people whether they know of any instance in which such a thing happened. They change the subject or get angry, as if I'm advocating rape. But I have yet to hear of any incident like the ones they fear. In my experience cross-dressers--let alone trans people--are in bathrooms for the same reasons most people use them: We take care of business and, perhaps, fix our hair, makeup or clothing. And, if we enter with someone we know, we might chat or gossip.
On the other hand, plenty of trans women--and men--have been assaulted in bathrooms. A trans woman in Washington DC is one of the latest victims. She was attacked in a restaurant in Dupont Circle, in the northwestern part of the city.