I don't really get the posts saying his performance last year was good. It wasn't. For a player this long in the league, he should be better. He regressed and proved himself a fluke. And numbers aside, watching him in a game, it is pretty clear that even after all this time in the league, he still doesn't understand plenty of situational basics. If a QB doesn't understand the play that is called and doesn't run the play the right way, but lucks into finding an open receiver who breaks a tackle for a 20 yard pickup, the QB's numbers are going to look good. But he's still going to get yanked by the coach. After his second season, once teams figured him out, he grossly underperformed. Anyone watching the team could tell you that. And, as Stadler points out, it is a MAJOR issue that he isn't a "system" guy. But going back to the time he was successful, another strike against him is that even during that time, a lot of fans as well as people around the league started really being put off by his surly attitude. Not sure if that was something Harbaugh taught him that he latched onto, or if that was him (he really didn't seem to be that way in his first year, and seemed pretty likeable). But he started to alienate a lot of people long before his protests. You put those two factors together, and I think he is automatically going to have a HUGE hill to climb in terms of getting signed. Add in the major distraction he has become, as Kev pointed out, and I can certainly understand him not getting signed.
As someone once said in a job recruiting seminar that I went to: "When you are interviewing for a job, the boss wants to know two things: (1) can you do the job? And (2) are you going to screw up the boss's day and make him/her have to devote attention to you that he/she would much rather spend doing his/her own job? If you want to get hired, the answers better be 'yes' and 'no,' or there will be a better candidate every time." There's a lot of truth to that. Kaepernick doesn't do the job all that well. And he requires too much of the boss's attention. I would pass on that candidate every time, even if there wasn't a better candidate available. Better to have a vacancy than make a bad hire and have to deal with cleaning up the mess that that creates.