Because NFL owners are quite stupid even by the water-brained standards of the ultra-rich, they devised a strange sort of tiered non-compromise compromise on the protests in the hopes that Trump would stop ranting about their league and the ungrateful, un-American, subhuman thugs who are both its labor and its product. They did this without the consent or even the input of the players, which displeased the players. And Trump, because he is Trump, did not accept the deal. He’s a man who only knows how to do a couple of things, but one of those things is to find a bruise and then push and push on it. He does that very well.
Sportsball might not matter much, but it's helpful tale to understand many things that do. The only thing that will stop Trump harassing the NFL is if he finds a new racist thing he likes better. And even then probably not. Also, too, why should they care?