The further I go in this career I realize that it is an excellent medical school (I am not claiming it is top in the nation status) but I do think they have pretty unique admission criteria that don't always make sense (at least from when I was there) that can make people feel jilted.

I also don't think there is an obvious bias against BYU/Mormon students from the administration. I personally think a lot of the perceived bias is due to the fact that there are so many excellent students applying to medical school out of BYU that rightfully feel they would be good candidates there (as evidenced by other acceptances that are maybe more prestigious) but get rejected due to the crap shoot that med school admissions ultimately come down to. That or that the school cares less about MCAT scores/grades than other schools might.