Is there any fan base other than Utah's that merits such strong negative emotions?

Consider: USC students have little reason to hate BYU fans in particular. The two schools have played 4 times, splitting the games, and last time USC came to Provo, they were probably gifted free ice cream. BYU fans have never been to LA while these students have been in school.

Also consider: the most popular, instant association most people have with the State of Utah is "Mormons," even though many Utahns obviously are not LDS. The USC student section in particular showed themselves to be fairly ignorant, in that they chanted a slur against the religion to which their own QB belongs. It would not be surprising for them to assume any Utahn with whom they associate is "Mormon." Note that the University of Utah has "Utah" in its name.

Now consider: Therefore, most of USC's perceived interaction with members of the church (however true or untrue) is via regular games against Utah. Those games involve a fan base known for things like pooping in their own stadium's concourse, offering alcohol to children, cheering for drunk women to strip, pouring beer on opposing players' families (as recently confirmed), etc. Not a fanbase known for positive behavior. There is undoubtedly overlap between such fanbase and the Jazz fans known for racist harassment of NBA players, etc.

In conclusion, not only is it reasonable to conclude that USC students were chanting slurs against "Mormons" based on their interactions with Utah fans, but it is almost certainly the only reasonable conclusion. In fact, until proven otherwise, this conclusion is unavoidable.

Therefore, not only was USC's apology merited, but the University of Utah, and specifically student leadership of the MUSS, should apologize to BYU fans for these slurs without delay. Every minute they wait is a minute their actions implicitly endorse bigotry and intolerance.