From my experience working with in a couple of different athletic programs I have couple of things to say about this:
1) It's a requirement for every athletic department to self-report a certain amount of violations every year. Basically the NCAA rule book is so vast and complicated that if you're not violating some rule at some time that looks more suspect then if you actually tried to follow all the rules.
2) I would bet a large sum of money that the same, if not worst, violations (based on what has been reported thus far) were taking place right now at every division I program in the state of Utah. Especially the University of Utah since they have a much larger budget, play in a power conference (keep up with the Jones or in this case USC, Oregon, and UCLA), and have less institutional restrictions placed upon the athletic department.
3) Predicting what punishment the NCAA will hand down, if anything, is like trying to predict where lightning will strike. The NCAA does not have a track record of following their own precedent. Where BYU is self-reporting the violations and will likely submit to their own punishment along with said report of violations will probably be the end of it. Of course if there is more to the story then what has been reported so far then of course the NCAA will come down harder. But one thing to consider is that the NCAA very recently has had a bit of a black eye when it comes to PR and student athletes (Napier saying he goes to bed hungry and the Boise State football playing being homeless and no one could do anything about it cause it was an NCAA violation among a wide range of other things). If all the guy on BYU's staff was doing was giving discounted rent and such my guess would be that the NCAA won't be extremely harsh. Now if there is more (and it possible there is especially considering how long it went on) who knows what will happen.
4) It is completely possible that Bronco Mendenhall had no idea it was going on. Consider that a head coaches has to manage a staff of at least 20 coaches and admin plus 80 to 100 student-athletes. No way it is possible that he knows everything that is going on with everyone. Also, these athletes aren't dumb. If Bronco is as much of a rule follower as he is made out to be the athletes aren't going to go telling all the coaches and such. Also it is unlikely that other players will snitch on their teammates.