Yeah, that happens constantly, especially if a story is strong enough to be considered "alive" in that metaphorical way.  The thing with the protagonist: he/she doesn't have to be the central character, but he/she does have to be the character whose viewpoint the story is told from.  That's really all that makes the protagonist.  I guess you could say it's just a matter of page-time.  Protagonists don't have to be the "central" character; I've read some stories in which the protagonist was simply the observer.  I've read others in which the protagonists are passive characters and the other characters get to have all the fun.  I've certainly written stories in which the protagonists were passive, and the only thing they offered was a way for the reader to enter the world of story and care about the events and characters depicted.  If your story does that, it doesn't really matter who the protagonist is (on one level).  The thing to consider is how the story is written: even if your protagonist is not  the main player, the Top Dog or whatever, he or she should be the one that provides the context of the story.  If written in first person ("I") then it's a lot easier for the protagonist to be someone other than the alpha-male or whatever.  From 3rd person ("he" or "she") it's just as easy, but the viewpoint should probably be 3rd Person Limited, which just means that as the writer of the story, you limit insights, perception, actions, etc. to that character, and so the reader wouldn't know any more than the protagonist knows.  And that's the funny thing about protagonists, they aren't always the central characters, but they are the central viewpoint characters.  A perfect example would be Moby Dick.  Captain Ahab was the guy that got all of the action, but Ishmael was the guy telling the story, thus Ishmael was the viewpoint character, but Capt'n Ahab was the protagonist.  In a later novel, The Scar, by China Mieville, the central character, Bellis Coldwine, was immensely passive; she went along with the main-stage players, existing as the conduit through which the readers were able to enter the world of the novel, but everybody else got the juicy, dramatic bits, and she existed simply as either an observer, or the person who actually survived the whole thing simply because she wasn't constantly risking her life.  Now, in my own writing, I sometimes consciously avoid letting my protagonists and central characters be the same person, but all in all, it depends on what you want your story to be.  If your protagonist differs from your viewpoint character, this opens up emotional possibilities that simply don't exist if the viewpoint character and protagonist are the same person.