not $3B. Although after doing a Google search, a lot of anti-Mormon yewt fans like to claim that City Creek cost $3B or even $5B, but that is neither here nor there.
The biggest issue is that the church considers BYU athletics one of their biggest missionary tools. According to several of the 12, the list goes as follows: Missionaries, MoTab, BYU. Before you go all yewt and not understand marketing, that does not mean that people hear MoTab or watch BYU athletics, they want to get baptized (although I had a tracting baptism where the first words out of the guys mouth were: "Jim McMahon played at your church's school. Come on in."). BYU athletics provides exposure. Especially exposure to a demographic that the church really struggles in.
The church spends a lot of money on MoTab. I don't know exactly how much they spend annually, but I guarantee that it dwarfs BYU's athletic budget. The church subsidizes for MoTab. I would be thrilled if the church would at least subsidize the non-revenue generating sports at BYU. If they were to do that, BYU football and revenue would likely post a $20M a year revenue as opposed to the $5M that they currently post. That revenue is then put back into the programs each year making them more valuable and able to pay for better coaching and facilities. BYU's success and the success of their players then produces more exposure for the church.
At the very least, the church needs to stop tying BYU's hands behind their back when it comes to athletic fundraising.