NASCAR, hunting, and fishing are red sports. The NBA and Formula One are blue sports. Most other sports are in the middle, including the NFL.
Given its violence and military analogy and the facelessness of the players, you would expect the NFL to lean a bit to the red side, and it does. However, it has plenty of blue fans, including me, and times are changing. Many of the players are African-American, and the recent revelations regarding safety are a long-term threat to the viability of the league. The NFL, in short, doesn’t need any more sources of controversy right now.
Trump probably thought that commenting on national anthem protests would play well with his base, which, of course, is the only thing he knows how to do. The impact of his comments, however, was to unite the players against him, and the owners, who are natural allies of his, were in no position to resist under the current circumstances.
The bottom line is that the NFL isn’t NASCAR, and when Jerry Jones, Bob Kraft, and Tom Brady disagree with you, you know you just screwed up.