The fact is that the judges at the time voted BYU as the #1 team. The judges of 2004 and 2008 simply didn't do the same for Utah.
That's like undervaluing a gold medal for an athlete because the silver medalist of a different year performed comparably. The fact of the matter is rankings are necessarily relative to the competition at that time. Just like the first gold medalist did the best that year, BYU got the championship.
Utah did well, but not well enough relative to their competition, and got the silver medal. They did not win the gold, only Ute fans would pretend it was.