I think reasons could vary but could stem from the view that if you don't go to BYU it's because "you didn't get in." My wife and my little brother both had scholarships to BYU and chose other schools. They had BYU alumni members in their wards question this decision and a couple even expressed high disappointment. That's my view because of their experiences.
That said, I'm one of many that are pretty apathetic or actually supporting to BYU's success but when they play Boise, I cheer hard against them. I was pulling for you over Nevada, that's a team we legitimately hate. Though a conference mate, we'd be ok with them losing every single game, every single year. Hate their fans.