The right to protest cannot be abridged by an employer. She is making a political statement, not criticizing her coach. The national team is not the United States Army. She is not operating in a war zone. She has a right to make a statement. And kneeing, or in some way protesting in a way related to the flat is not a crime.
Indeed, the commander-in-chief, Barack Obama, has "called Kaepernick’s decision to kneel down during the national anthem an 'exercise of his constitutional right', and commended him for standing up for an issue he 'sincerely believes in'." So it makes little sense to criticize Rapinoe for doing the same.
An interesting response, but you were legally erroneous from the first line. Yes, employers CAN abridge, control, or influence an employee's on-the-job communications, be they in protest or communicating most anything else. Try wearing a "Dump Trump" tee shirt to your sales job at your local mall store and see where that gets you.
"The first thing to know about the First Amendment is that it is a limit only on government. It prohibits the federal government from making laws that infringe on the rights of religion, speech, press, assembly and petition. Through the Fourteenth Amendment, state and local governments are also prohibited from infringing on these rights. Yet, one of the most powerful restraints on individual freedom is the power of employers to discharge workers. If your employer is a private entity, the First Amendment offers you no protection from being fired on account of what you say. (You may still have protection from other sources described below, or in the one state that abolished employment-at-will, Montana)."
As to the President's remarks, context is important. My guess is that he referred to CK's ideas as free speech, not the protest itself. The "performance" of NFL football belongs to the NFL, not to the players, at least not yet. Only if the player is protected by the terms of the CBA do they not risk reprisal. As we move forward, you'll see these pre-game behaviors become part of the CBA. That's if the playing of the anthem continues in the present manner.
You said, "So it makes little sense to criticize Rapinoe for doing the same." Frankly, I didn't. Similarly, much of your opening paragraph is so loosely constructed that it's hard to respond to it at all.