While I do agree with you, and I follow the same logic as you -
I don't have a problem with other people who do feel the need to express themselves every once in a while. I come from a very vocal group of people (my family and friends consist of hippies and punks), so I say if you have something to say, say it. I may not do this, but I would never penalize others for it.
Just so everyone knows, I see how it could get really annoying after a while if they kept making comments, but I really don't think they mean to bother anyone in the attraction.
People applaud during other attractions as well that don't ask you to - (and I've heard many "boo" Gaston in BATB), but if it's okay for people to applaud in other attractions, I don't think it should be a problem to applaud of boo in this one. I'm just trying to be fair here.