I agree! I've always thought that Harry was really brilliant at some times in the books, and brilliantly clueless at other times when he really could have used his cunning to protect himself.
I always felt he had it in him, he was just so used to deferring to others--the Dursleys, Ron, Hermione, Dumbledore--that he didn't allow himself to question all of the inconsistencies in his life.