BYU is not the most popular school in the state. It very likely was at one point but Utah has surpassed it. From a 2016 public policy poll:
"Utah wins out over BYU when it comes to college sports loyalties in the state, 32/26. Utah State is third at 16%, followed by Weber State at 4%, Southern Utah at 3%, and Utah Valley at 2%. There are massive political and religious divides on college loyalty. Among Democrats Utah leads with 54% to 15% for Utah State, with BYU only tied for third with Utah Valley at 5%. But among Republicans BYU wins out with 40% to 21% for Utah, and 15% for Utah State. The political divide mirrors the religious split- among Mormons, BYU leads with 40% to 20% for Utah and 17% for Utah State. But among non-Mormons Utah romps with 55% to 14% for Utah State with BYU registering at only 1%."
Other broader and more informal polls generally show the State of Utah as being largely Utah fans outside of Utah County, which is pro-BYU, and Logan, which is pro-Utah State.
As for national fanbase, I would assume the numbers from the above-referenced poll would have some merit there as well; i.e., LDS folk who do not have geographically-based loyalty to another school (e.g. I live in Columbus, Ohio so I tend to support Ohio State) or an alma mater-based loyalty to another school may have (or likely do have) an inclination to support BYU because of church affiliation. It is very unlikely that BYU has any significant national fanbase with non-LDS people because it can't even garner that in its home state.
So, no, BYU is not the most popular school in Utah, and any national fanbase it has is very likely entirely linked to LDS church affiliation. I suspect a significant factor in Nacua's decision is the kind of exposure he will get to NFL people, and while the ESPN deal is a bonus for BYU (as well as non-Pacific time kickoffs), Utah and Washington offer the change to play in Pac-12 championship games, Rose Bowls, and other big bowls with Pac tie-ins, as well as a full slate of Power 5 opponents each year.