Yes, there's people that just hate BYU more and that'll probably always be the case. But over the last 10 years I can tell you from both personal interactions and online that there are quite a few who now have a greater hatred of Utah than BYU for exactly the reasons you mentioned.

The crap they've pulled ever since getting sloppy-seconds into the Pac-12 has been unreal and a chunk of their fan-base went from "It's ridiculous the way P5 members think they're better" to "We're P5 and shouldn't condescend to play those guys unless it's 100% on our terms." And you'll note that USU has not contracted to play Utah since they joined the Pac-12 (the games played while in their new conference were signed before).

I think the administration largely feels the same way. Sort of a "We're happy to play, but if you think we're gonna do a 2 for 1 or a body bag game when you're doing home-and-home with SDSU, Wyoming, and Northern Illinois..... forget about it."