Whether or not you like Utah, they're not fundamentally that different from an Iowa or a Wisconsin or a Cal or a Texas or New Mexico or Colorado or Wyoming. They're a large state university. Some of them have more football tradition, some less. Some are stronger academically, some less. But they're all broadly in that same grouping.

BYU is unique and therefore stands out more, which leads to additional dislike. Not because of religious reasons (for most at least), but because we're different. So people note playing BYU more than playing "another state school", and BYU is absolutely easier to stereotype than another state school.

I will say though that I disagree on the higher academic standing thing. BYU is certainly stronger academically than Utah State or Utah (especially for undergrad), but (by many metrics) the gap isn't that huge at this point and BYU actually rates below the median among P5 schools. I think that inflated sense of academic self-worth has turned off more than a few people as well.

In the end it's not something you can blame solely on the actions of BYU students and it's not something you can solely judge on preconceived and unfair notions from other fans. Both play a role.