Exactly what is stopping your six year old son from wandering around the bathroom and/or leaving the restroom while you are in the stall? What is stopping someone from taking your son while you are in the stall? Why is he any safer unattended in the bathroom or unattended outside the restroom?
As a daughter, wife and mother of a son, I resent the heck out of the idea that men's restrooms are molestation central. I assure you that if anyone tried to do something to a boy in the restroom, my dad, my husband or my son would be right there intervening.
Well as wife and mother of not one but 2 sons, I do not resent it in the least, don't know why in the world you would.
Now, boys have been molested in bathrooms for a very long time, it is often" no, but it can and does happen, in fact they have been murdered. Now not at WDW, that I know of. Also these boys were molested and murdered when the restroom was empty, again not at WDW.
Also mine would stand right outside my stall and not move, (good parenting) if you can't control your child, then maybe don't being him out at all. And if someone tried to take him, I would see it and trust me, they wouldn't get far, unlike being in a men's room with just a couple of other men.
I think the problem is, at WDW it is a much busier place and these types of things most likely don't occur. The only problem I have with sending in a younger child at WDW is that some of the bathrooms have multiple exits and can be confusing and a child can get lost.
I can tell you that there is no way I would ever send in a young child to a bathroom in certain areas and venues, to do so is nothing short of bad parenting, IMHO.