Its very easy to get good grades in weak majors...You really can't compare university to university. A better comparison would be of different programs. For example comparing the Marriott School to the Eccles and Huntsman Schools... But comparing BYU to UU on overall programs doesn't really tell much of the story. At the end of the day, a degree is a degree and C's get degrees.
The reason for this could also be how entitled, and unrepresentative of the student body the Football team is. I only know a few members of the team, 2 of them are rather undisciplined, out of shape linemen who I view as bullies... Its just a matter of atmosphere...