The fact is, most BSU fans in Idaho who aren't also marginally BYU fans have a significant level of disdain for BYU. I think that some of it comes from the years where BSU was an FCS school, and they felt (rightly or wrongly) like Idaho BYU fans looked down on BSU or felt superior to them somehow. Some of it also just comes from being a "regional rival". Whatever the reason, a lot of BSU fans really, really, REALLY dislike BYU.
For Idaho BYU fans who grew up rooting for BSU, or who "hopped on the bandwagon" at some point, they refuse to acknowledge the fact that a lot of their fellow Bronco fans act like real turds to BYU fans. I've had a few who at least acknowledge the fact, but use the usual "it's just a few bad apples" excuse for their behavior.
For the record, I'm not saying that the BSU fans are at Yewt-level degeneracy, but it is certainly more than a "Few bad apples".