common in our house at least :) i carry hand sanitizer because not only is my son afraid of the flushing, he refuses to wash his hands if (like at walmart) the automatic sinks have warm (actually really warm, almost hot) water coming out. and forget about the air dryers.
i kind of just deal with it. i do flush, and he has to deal with it. i will wait until he is out of the stall. but it is a pain, trust me, i know! but it's not something i'm willing to cater to him on. it's just noise. it doesn't hurt them. we are all afraid sometimes, and we still have to do certain things, like flush the toilet. i don't really see it as an option.