I think it goes back to a few things:

1) The Church spends its money where marginal benefit = marginal cost. Although you might not perceive the value of some of those expenditures, it doesn't mean that they're wrong. The Church has more information and a wider vision than just one individual (or a group of fans) with an opinion.

2) The Church has invested in BYU and the football program. It's a top 30-35 program. If your vision is that the program is bigger and better, then it's on you (and the fans) to make it happen because the Church has already decided (#1).

3) BYU fans, on the average, do less to support their program than fans at other "top tier" universities. I've experienced it. I've seen it. The status of the Cougar Club is evidence enough. You want something to change--make it apparent that there's demand. Donate money, go to games, invest the time and effort.

Personally, I wouldn't feel comfortable with the Church joining the arms race. I think that the spending in big time college football has gotten ridiculous. If the fans want to support the program and the salaries, then I'm totally cool with this. It's the same thing that happens at other schools.