Rankings are biased. Rankings are flawed. EVERYONE agrees on this. The season before often unfairly inflates or undervalues a team. Yet all of the sudden that is the deciding factor about whether a season was good or not... When you first get ranked? All it takes for a team like BYU is to have an early season loss, and they won't see the rankings until late in the season, which is exactly what happened in the years you are talking about.
In the end it comes down to winning the games, Utah won them... BYU didn't. Does that mean BYU sucks? Does that mean BYU should fire everyone and start from scratch? Obviously you think so, and someday you will get your wish. I personally feel there will be a day when you look back and wish BYU still had Bronco Mendenhall as its coach.