I don't generally like silent protagonists. It makes no sense to me why someone wouldn't say something in reply to the many many times that they are spoken to. But then, I am one of those rare people that doesn't mind cutscenes, so that might have something to do with it. I prefer my protagonist to have some character, not just be an empty shell.
EDIT: To clarify somewhat, I hate silent protagonists when they're in a game where they clearly oughto to be talking, such as a lot of first person shooters; in the majority of those games, I feel that the protagonist should definitely be responding when other people talk. In games where there generally isn't much dialogue anyway, I don't mind. For example, it never bothered me that Chell doesn't talk in Portal, because there doesn't really seem much need for her to be talking anyway.