Or Oregon. Or South Carolina. Or USC. etc. etc. Even if Virginia and Houston went on to be horrible teams, it doesn't really matter. All it takes is a team having 2 or 3 guys that gives the other team matchup problems, and you probably have a game on your hands. Doesn't matter who you are. Just win. USC couldn't contain BC's QB, despite the fact he can't even throw the ball, and they lost. But they'll beat many of these Pac teams that are ranked cause they don't have QBs that look like Usain Bolt out there. That's just they way it is.
BYU is not a perfect team though, that's for sure. They don't pressure the QB well and QBs that can read defenses can pick them apart. I really think BYU's defensive philosophy is built around QBs sucking. And it's probably a good bet. There aren't many college teams with QBs that can throw it around well enough to beat them and that also have the defense to stop BYU's offense.
BYU should definitely be ranked. They have looked good for the moments I have watched them. Hill is probably the 2nd best dual threat QB behind Prescott.