While I agree with the Y being a better academically ( went to both schools and graduated from the Y. I am a cougar through and through), the real reason we have more of a national fan base is the fact that for the past 100 years LDS and non LDS alike are able to go to BYU institutions without the state imposed constraints (out of state tuition) that other schools deal with. That means that while they are able to attract recruits from out of state, the student body is largely Utahn. The fan base are Utah transplants where with BYU students go back to their roots. This is a hugh advantage for a team who is growing a national following. This is how Notre Dame also exports its sports programs but to a larger audience then that what BYU has.
Nevertheless, it is an advantage that Utah will never enjoy . . . and can't.