The actual number of cases is probably one of the smallest per capita in the world, because it is BYU.
However, if you are talking about under-reporting, which is a problem everywhere, I would say BYU has been one of the worst, because almost no where else do you have the additional hurdle of a strictly enforced HC where students are expelled for just having sex, or several of the other honor code breaking activities, like drinking alchohol/drug use, that often contribute to higher incidences of sexual assault.
Until today, there was a huge barrier to reporting a sexual assault, in addition to all the other typical barriers that victims experience, not withstanding that perpetrators were using the HC as a weapon against their victims to not report, as was mentioned in the newspaper articles.
In 2006 & 2011 BYU reported 0 sexual assault cases, with 30K students, you have to have your head buried pretty deep in the sand if you think that is a reflection of reality.