I think what troubles some people is that it comes over in a dictatorial fashion. We all know that most of the TSA setup is for show, and we're all tired of being told our bottle of water is an explosive (yet same explosive is available at Hudson News for $4).
Further, it's drilled into our heads that the crew and the crew's instructions are there for our safety. And I know it's not the intent of the pilots, but when you have smooth air and to use something that is supposed to be there for our personal safety, the seat belt light, only for one or the both of the pilots to use the bathroom, it does come over as a little "cattle" like.