The NFL has always been a long term strategy. They've also been mostly good in toeing the line when an issue comes up that's sensitive, and waiting to pick a side until they absolutely have to. Just take a look at how domestic abuse situations were handled when they used to occur, versus how they occur in more recent incidents. Much less tolerance and appropriately so.
The NFL will allow peaceful protest because they are finally recognizing that the players are the ones who have the power. The players, again, predominantly people of color, have recognized as many other groups of people have recently, that they are the blood of which the big machine runs. There is strength in numbers and the players hold more cards than the owners do, but getting enough people on the same page to organize and demonstrate effectively is the hard part. The people and the players have had enough of the blind eye being turned to this issue, as well as it being covered up under the bogus framing of being non-patriotic or whatever.
The NFL recognizes that the old, conservative, racist demographic which it has relied on for too long now isn't going to be around a whole lot longer. At least not in a majority sort of sense as it has been. If the league wants to be an organization that younger people, who are far more socially aware, tolerant, and understanding compared to the generations before them, feel like giving their time and money to, this is the only approach to take, and it is right and it is long overdue.