The NFL has no rule requiring players to stand during the national anthem. So, yes, Kaepernick is allowed to make his own rules in this regard.
It would be like an accountant drinking from a “World’s Greatest Dad” coffee mug instead of a “God Bless America” coffee mug at work — that’s the worker’s prerogative. Or bringing a tuna sandwich for work instead of a ham sandwich — since the employer has neither prescribed nor proscribed any particular type of sandwiches, the accountant is free to make his own rules.
Of course, the 49ers are free to bench or cut Kaepernick. Or the NFL can change the CBA next time around to provide for the banning of a player who participates in any sort of on-field political demonstration. And if you feel so strongly about this issue, perhaps you should lobby one of those organizations to take one of those actions.
In any case, your sense that a sporting event is somehow a “non-political arena” is sorely mistaken. Politics is deeply rooted in professional athletics. The fact that NFL games play the national anthem at all is a political act—so Kaepernick’s sitting during the anthem is merely a response in kind. And have you seen those gaudily massive American flags that they’ve rolled out during the anthem? So very political. It just happens to be a political gesture that you seem to support.