Whether you agree or disagree with Kaepernick, he most certainly isn’t only protesting the song itself. He’s protesting the idea of American citizens pledging their unwitting allegiance to a flag under the banner of which many people are still unfairly oppressed by the machineries of the state: that it is only the land of the free for those lucky enough to not offend a police officer’s sensibilities by being black, and only a home for those whose bravery might include being a soldier, but does not include being a Muslim as well. He’s standing up for an America that everybody — left and right alike — says they’re committed to: one where a person can go about their private business without undue interference, and really have the inviolable rights that were part of the fight made by people like Frederick Douglass (who died well before state-level attempts to disenfranchise black voters were outlawed, and 25 years before women of any color won the right to vote.)
Some protest the government by storing weapons in preparation for Armageddon. They get a whole amendment! Some protest by launching desperate, filthy attacks to delegitimize those in power based on conspiracy or untruth. they get nominated!
Propagating the idea that sitting down is suddenly the most offensive form of protest imaginable strikes me as deeply un-American and, yes, unpatriotic.
(edit to add “only” in the first sentence. I re-read and realized it wasn’t clear)