I think the flags they threw were, at least for the most part, justified.
My main beef at this point is that they were inconsistent at times, particularly regarding holding by the Virginia Oline, as you said. So I feel the problem with the officiating was the flags that weren't thrown, rather than the ones that were.
But there is no question that BYU committed a bunch of PI fouls, and also did plenty of stupid things that led to the dead-ball penalties. I'm afraid we deserved most of what we got from the refs. Need to be smarter about that.