The biggest threat to the NFL, football as we know it, is lawsuits.
IF a lawsuit is successful in establishing that the NFL is liable for injury caused its players because it has faciliated a violent game and not done enough to protect the participants, the game as we know it is OVER. Because once the precedent is set that you are facilitating a dangerous activity and responsible and required to take all measures to protect participants, it is nearly impossible to take all necessary measures to protect the players without so altering the original situation as to render it unrecognizable.
I know most people would argue that the players are participating of their own free will. Similar to bungee jumping right? You sign a waiver acknowledging the risks, the operator takes all reasonable precautions for safety for an activity the participant acknowledges is dangerous, and you jump. If something goes wrong, the operator is only liable (and their insurance liable) IF the operator is shown to have done something negligent.
BUT, it is inherently different than bungee jumping in one key facet, the operator in the NFL's case is PAYING the players to participate in the inherently dangerous activity. And paying them an amount of money that could be shown to sway even a reasonable person not wishing to risk injury to take a chance they would otherwise have avoided. Moreover, a good lawyer would show that the payment to the players in many cases took advantage of people economically less fortunate, and with few other options to ever earn this type of money, to encourage them to take this risk (of course, at the NFLs pay scale, this would apply to almost everyone
This is what the NFL knows and is scared to death of.