First, utah football did not finish decently unless you consider 6th place in the conference decent.
Second, 'Do you think that the church isn't funding or substantially subsidizing the athletic program and the TV exposure for BYU?' The church does not fund the athletic program. It is self sustaining from tv revenue, ad revenue, donations and ticket sales. However, BYU is in a very good position financially with their athletic programs relative to nearly every other university.
Finally, you are correct on utah's other programs being a disaster in the pac12 right now and with the need to improve or even build facilities for those programs, the additional tv money will get siphoned off very quickly once they even start receiving it.