I think some fans remember how good Kapaernick was early on in his career, but forget how mediocre he was later on. If he had still been playing at a high level, he'd still be in the NFL, anthem protest or not. If you don't believe that, ask yourself why Eric Reid and Michael Bennett survived.
You can get mediocre quarterback play from a lot of guys, as any Bears fan well knows. If you sign a mediocre Kapaernick, however, the media circus comes to town with him, and disrupts your practices and locker room in exactly the way no head coach wants. And it seems Mr. Kapaernick is more likely to stoke, rather than douse, those fires.
Which is likely the biggest reason he's still unemployed.
Note that the NFL, and not some individual team, wanted this workout to happen. PR, anyone?