I'm taking Jaws Unleashed and Okamioff this list, since the heroes of those games are wild animals who would not be expected to talk. Sure, Amaterasu is a goddess in disguise, but the mortal form she chose is that of a feral wolf, complete with howling at the moon, urinating on her enemies, and an inability to speak. This goes double for Jaws, who is a fairly ordinary (if really big) shark.

I'm leaving in Ecco the Dolphin because while dolphins don't normally speak, the ones in that game speak to you, so Ecco remaining silent is still out of the ordinary.

    I guess it depends on what you mean by "talk." If an animal protagonist meows, barks, growls, howls, etc. then I wouldn't have it as a silent protagonist. Since Amaterasu at least howls, I guess that would make her a candidate to be taken off the list, not because she took a wolf form (For the most part, when higher beings take on a form like that, most of the time they can talk, so she would be an important exception).
    I think putting an extra requirement of "they have to talk (I'm inferring you mean talk as speaking a language)" or "be a species that has to talk but he or she doesn't " just makes the rules for putting them in unnecessarily complicated. For Jaws, is he the protagonist of the game? I think so. Is he silent? If he is (I didn't play the game, so I don't know) then yes he's a silent protagonist. He does fit the description. Concepts already have enough hidden assumptions, let's not add more.