It doesn't bother me but then I don't see it as a particularly personal thing to do. I don't think I rubbed my bump much unless it was painful, I did rest my hands on it a lot though.
I rested my hands, cups of tea, my dinner. A baby bump is so convinient.
I agree I think it's subconscious a lot of the time and also protectiveness. I know that if ever I was in a crowd, for example I was heavily pregnant over Christmas and had to face the xmas rush, I would always have a hand over my bump to protect it.
I used to just sit in my office chair with my hand on my bump looking down and seeing/feeling it move, I loved it!