S.T.
Get him to an audiologist or an ear nose & throat doctor. Sounds like this is a problem with his hearing and it sounds acute.
My kids were afraid of the auto-flush toilets because when they're so little the auto feature thinks they're off the toilet and it begins to flush while they're on it. But this doesn't sound like a problem with the toilet as much as a problem with the hearing.
When you're not anywhere near public toilets and he's in a comfy secure place ask him about what scares him or makes him feel yucky when you're at a public bathroom. Give him the last example - "remember when we were at ________ and you were upset while sister used the toilet? I want to figure out what we can do to make sure you don't get that feeling anymore." then ask, does it hurt your ears? does it scare you? does it make you remember a time when you were scared?
Kids are so funny, the conclusions that they draw can be so very different from what we expect. Once you know what's causing his strong reaction then you are halfway through the battle. Make sure he understands that you are going to do everything possible to protect him and make this better but you need to understand it and you need HIS help to understand.