Your argument seems to be that the two things are dissimilar because flipping the bird is always misconduct, while kneeling is only misconduct in one set of circumstances.
Kneeling is also misconduct if the player is a homosexual and is sexually harassing or taunting a heterosexual teammate.
Then, too, a player bantering with a teammate in the locker room can use “the bird” without offense.
Well, yes. The two things are dissimilar because one of them is almost certain to be considered "misconduct" in a legal proceeding -- while the other one is not likely to meet any objective definition of "misconduct."
This is why written rules are so critical in any labor dispute. Labor law does not look kindly on any type of disciplinary measures that can be construed as being arbitrary in nature. Without documented rules in place, a player who kneels during the national anthem is likely to be considered no less respectful than one who closes his eyes or looks down at the ground.
The problem is consistency of situation. Flipping the bird is always the same message, a message that is not generally considered protected speech in most employment circumstances. Kneeling is not. Tebow kneeled during the anthem through his whole career. Now he was kneeling in prayer not in protest, but it immediately shows the problem with trying to say kneeling is bad. It’s a certain type of kneeling with a certain intent which players could easily nuance, especially if goes to court. Unless behavior during the anthem is codified in the rulebook and CBA (which is only the case in the NBA) trying to after the fact declare some behavior misconduct is doomed.