There are many problems in the NFL. Sure labor is relatively tame right now, and fan interest is near the peak. But the problems are plentiful. Referees locked out. Lawsuits. And Bountygate dominate the headlines.
But lets take a look at how they got here.
Back when Michael Vick was involved in his dog fighting case, the NFL feared that Vick might harm the game much more, because the allegation was that he was bankrolling a gambling operation. That could have been a black eye, and the NFL dodged it.
Then came Spygate, and Goodell made a decision that the prospect of cheating in the game could taint the game, and maybe have a broad impact. He was admonished by senators, the FBI, and the DOJ for destroying evidence and the possibility of obstructing justice. But he took it to avoid at the very least a PR nightmare, and at the worst the fall of the game from grace. There has been some recent movement suggesting that the Patriots team also had some additional communications systems in helmets, and certainly the NFL hiring "communications consultants" to monitor radio frequencies at games suggests there was at least a possibility of that happening - but this was never investigated (no doubt Goodell smiled over his good fortune).
And now comes the Saints bounty program. While the coaches being involved is bad, and their suspension is merited, the inclusion of the players was always questionable. Sure, its possible they were scape goats. Its also possible that Goodell had evidence to support they somehow were involved with the guy outside the NFL - remember the twice-convicted felon - who was contributing to the pool. The thing is that we'll never know. Goodell has - it seems to me - a real problem here because he does not want to reveal specifics for fear that the felon had some influence, paid players, or somehow (because games happen across state lines) that there is an implication of racketeering.
So Goodell acted as judge, jury, and executioner in handing down punishment. Only the players fought it, and won. Now Goodell faces a new series of problems. He can retain the special master to review the evidence and work with them to hand out new punishments (thus revealing what he knows to some and opening up the door to possible outside investigation or at least a PR problem), or he can let it go. If he lets it go, it sets a bad precent for meting out punishment to players.
And worse, the legal challenge proves the NFL is vulnerable. All of these former player suits for concussions are now very real threats (I don't know, but can guess, that the NFL figured they could win these challenges, and now it seems less certain).
So the NFL is at a bit of crossroads and its not clear what will happen next. But there is no reason the NFL has to remain the most popular sport. There is always a chance that will change.