As much as Utah fans want to think they own BYU in football, they have lost 3 of the last 4 games head-to-head, and are only 5-5 due to BYU being terrible from 2002-2005.
The conclusion I get is that in general when BYU has a decent team (read: winning record), they tend to beat Utah. The point is that even with all the success Utah has had this decade they have failed to have a winning record vs. their rival.