Actually, the most plausible theory is that the NFL owners reviewed their options in great detail, and after consulting their legal team they concluded that any disciplinary action they took would constitute a breach of the collective bargaining agreement between the NFL and the NFL Players Association.
Legally, it's probably that the only thing an NFL team could do with a protesting player was bench him, or cut him from the team while paying his salary for the remainder of this season -- and even the latter action might have been a problem under the collective bargaining agreement.
Collective bargaining agreement won’t stop owners from declining to renew the troublemakers.
“...any disciplinary action they took would constitute a breach of the collective bargaining agreement between the NFL and the NFL Players Association.”
Even if that were true, they could have issued a statement to that effect, and saying that they held the kneelers to be moral lepers.
All NFL contracts have what amounts to a “moral turpitude” clause. If a player gets arrested or makes some social media comment that is detrimental to the team, they can cut him. If the owners had balls, they would have invoked it.
Collective bargaining is possible I think more likely is the collective hollering of racism that the media would have released.