If the gameplay and story go hand in hand, then a silent protagonist generally works well. Western RPGs are the obvious choice here because the story revolves around gameplay (in this case, choices). Jack in Bioshock is actually one of the best silent protagonists because of how important it was to set up normal genre conventions for the big twist to break. Although I think it would have been cool for him to start talking after the twist.
That said, I almost always hate silent protagonists. Gordon Freeman's inability to speak constantly took me out of the game. In Half Life 2 you have no effect on the story yet they give you a mute character anyway. Obviously that's not me smacking combine with crowbars, it's Gordon Freeman, and I merely control him as he follows a linear story. In Fallout, it's me doing what I want, which is the only reason why it's okay for my character to not speak. And Crysis 2... oh man... there were multiple times when speaking would solve a LOT of needless miscommunication.
Instead of developers defaulting to silent protagonist for every game that isn't an RPG, they should do what games like Halo and Crysis 1 did: Have a main character that's mostly silent but speaks when realistically they should. Complete silence in a linear story is unrealistic and very annoying. Just let them talk a little to make it feel less staged. giving a character a specific name, backstory, and motivation, but refusing to let them speak under any circumstance is ridiculous.