It doesn't really matter if the NFL rule book says players must stand.
In U.S. law, the players' First Amendment right to freedom of expression takes precedence. The NFL, an an employer, cannot abridge those rights.
By making a simple, dignified statement -- going on one knee -- briefly, the players are not doing anything irresponsible (like yelling "fire" in a crowded stadium), or  defaming or besmirching their employers.
Also:
It is clear the protest is about police injustice toward blacks. It is not about the flag,  veterans, or any other mom-and-apple-pie issues Trump wants to attach to this to stir up his base.
NFL players are 70% black, fans 83% white.
Trump is doing what he does best -- pitting different groups of people against each other, hoping he can exploit the resultant fear and confusion for his own benefit.
That is what demagogues due.