football program is on the cusp of a downturn. So if that's what you mean by are they in trouble, then yes. No program is immune to the vicissitudes of college sports, not even the blue bloods like Alabama, Ohio State, Texas, Michigan, or USC in football, or Indiana and UCLA in basketball.
But that doesn't mean they won't have good years again. Utah is well positioned enough they'll have good years again. I don't forsee Kansas or Vanderbilt levels of CFB ineptitude in their future (though I certainly wouldn't complain if it happened either).