As the French wisely say, Cherchez la femme, look for the woman.
In this case, the woman is hip-hop radio personality DJ Nessa Diab.She's a Berkeley grad, a very dogmatic outspoken Black Lives Matter advocate and a Muslim. She and Colin Kaepernick are engaged, and Kaepernick converted to Islam during the off season.
The two are reportedly planning what Kaepernick calls 'a traditional Muslim wedding.'
Pretty simple...boy meets radical girl, they find they have interests and ideology in common...except,it's haram, forbidden for a Muslima (a Muslim girl) to marry a non-believer. This is not to say that Kaepernick wasn't pretty far along the radical path anyway.
It's a real love story...not only do they love the same things, but they can hate the same people too. There are certainly a fair amount of patriotic American Muslims, but many Muslims here follow the Qu'ran which says their first loyalty aside from Allah is to the umma, the worldwide Muslim polity. And no one with much common sense would call the folks at Black Lives Matter remotely patriotic. So it all fits together pretty well.
Another part of the back story is that both Kaepernick and Nessa Diab have been agitating the 49er's to trade Kaepernick to New York, where Diab is based. Ideology aside, this might be Kaepernick's way of adding some fuel to the fire.
Kaepernick would have been traded months ago if he was willing to renegotiate his contract.