Silent Protagonist isn't so much about feeling connected to the main character as it is feeling connected to the story, and the protagonist is a communicative medium. The silence is a means to reduce conversational redundancy, yet still be able to convey information the characters might know (that the player would not) without it being an awkward 4th wall moment; and make the player feel the decisions they make are actually theirs to make, and thus have an impact on the story.
Conversely, think of how lame it is in a game to be given an option that the game won't let you progress no matter how many times you select that option. It's a total waste, and essentially the exact opposite of having an option oriented character with decisions to make. Furthermore, the lack of a direct 'voice' makes it plausible for these various decisions to be valid in how the player perceives the character of the protagonist. Which, when done right, works really well in rpg's as it gives the players a feel IN the story and not around it. Thats part of the advantage I'd say a game can have over say a novelization or even a movie. Take Xenosaga as an example of the opposite end of the spectrum. Here you have vocal characters that are over voiced so the few roads left to the player are either a) redundant b) uncharacteristic or c) lies. Toss into too many fmv's and Xenosaga just comes off as an obnoxious movie the requires button mashing to advance.
However, Cross's big mistake is not given Serge an alternative expressive outlet, which a silent protagonist still needs to have. Jak did (when he was an actual mute) Crono did, Mario did, and there are other cases too, but I think those are the most well known examples of 'silent protagonist' that have more good done than annoyances.
