Kapernick's freedom is in relationship to him and the US government, ...
This is an incorrect starting premise. If someone kidnaps and locks you in a jail, even if they are not the government, they have opposed your freedom, and then acted upon that opposition by imprisoning you.
The reasons why we could speculate about with political theory, such as a theory of natural rights--those rights we have in a state of Nature allegedly even without the existence of a government. [At least according to John Locke and other philosophers.] Each person has a right to control their own body, freedom of association, life, liberty, the pursuit of happiness, allegedly and generally speaking but of course when other individuals are concerned such rights may be in conflict. As for Kaepernick, his freedom to kneel (do as he pleased with his own body) was the default freedom since he had not agreed to any extra-contractural stipulations about standing, i.e. he retained his freedom and did not sell his body to his employer for that purpose. Likewise, if his employer tried to steal his foot, that would also be extra-contractural and in violation of his freedom. Persons who wanted to destroy Kaepernick's livelihood and apply harmful consequences to him because he had the freedom to kneel were in opposition to that freedom, hoping instead he'd be pressured against his freedom to stand. They did not want him to have freedom of a different opinion in front of them/on television.