Around the turn of the century and into the first decade of the 2000's, the Church began transitioning into a much more international organization.  With its majority membership outside the United States - and nearly all of those milllions of members not knowing or caring anything for BYU sports in general or BYU football specifically - the Brethren seeing BYU football as a serious missionary tool went by the wayside.  It's not like they advertised it, but demographically it's not that hard to understand.  Add that to the fact that there were already a lot of members in the United States who didn't care, and what you see is a change in the critical mass.

The glory days of BYU football were created in a period when the Church's priorities were very U.S.-centric; and to put a finer point on it - regionally centric within the mountain west and California.  That regional nature meant a lot of football fans in the Church's footprint.  Often it seems like CB's myopia for the glory days loses sight of these significant changes.

I also suspect that there is another side to the coin.  While they may not be too proactive or concerned about making BYU into a perennial powerhouse, they do recognize that BYU football still gets enough press that they proactively make sure that we do not have a repeat of the Crowton-era scandal.  IOW, it seems as though the attention now paid to the program at the highest levels is more in avoiding the negative than building on the positive.  And I doubt that will change.