Yea, my kids hate the toilet flushing sound also. It's very echo-like in the stalls and the flushes really are loud. They especially hate the automatic ones b/c they can't get out of the stall before I flush lol.
Wondering also- he may have sensitive hearing to certain frequencies....(in reference to hearing the elevators and the stall toilet flushes). You could always have his hearing checked at his next checkup. But mostly it sounds like a little phase that started with not liking the flushes. I just posted a question about my daughter going through a phase of being scared of being alone in a room at home. Also- I just remembered a weird phase my son went through around age 3 or 4- he was scared of cell phones lol! I think just being supportive and keep trying without being too pushy would be a good idea.
Talking about it before you go (like what it looks like, what will happen, etc.) before going in the bathroom might help. As a speech-language pathologist, I do this with kiddo's that are having difficulty with things (such as bedtime routine ,etc.) or are going to experience something new (such as a plane ride) and we make up fun stories with pictures (real or drawn) and "read" the story before the situation or routine happens to help prepare them and let them know as much information as possible. Also giving re assuring phrases or choices helps. For example, when you go in a bathroom that seems scary- you can repeat with him: "I can pee then I can go" ; or tell him that he can do the paper towel or turn off the sink all by himself (make it more about the not scary part); or repeat with him "if I get scared I can squeeze mom's hand". Sorry, just rambling-
good luck with future bathroom visits!!!