I heard a great explanation from Scott Zolak (former Patriots quarterback) on Boston radio on why Colin Kaepernick is unemployed. I have to paraphrase a bit here, because I don't have the transcript.
Granted, Zolak was never great shakes as a quarterback, he simply wasn't as gifted as you need to be to make a poor team a competitive or good one, but he worked hard, is able to see the issues with Kaepernick, and has talked with other quarterbacks off the record about Kaepernick's strengths and weaknesses, so I think his insight is worth considering.
When Kaepernick came into the league, and started the last five games of the 2012 season, the San Francisco offense was built to exploit him using the read option. It hadn't been used in the pros as more than a novelty or gimmick, he was tearing up a league that wasn't ready for him. He was nearly unstoppable because defenses hadn't paid attention to the scheme.
But eventually teams figure you out. Zolak talked about how after other teams had enough film on Kaepernick and the option, coaches would widen the tackles, putting them further off center, getting linebackers to fill the gaps, and taking a more patient approach, steering the quarterback into lanes where they would be able to tackle him. (Zolak says that defensive coordinators don't get enough credit for that aspect of the game. The negative performance is often heaped on the quarterback, when the truth is, defensive coordinators get paid to figure out ways to neutralize opponents strengths. And it is a copy cat league. One team does it...they all do it. It is a scheme adjustment, and once they figured it out (by the end of 2014/beginning of 2015 seasons) Kaepernick's days were numbered. He just didn't (and doesn't) know it.
Once teams figured out how to defend that, Kaepernick realized he wouldn't be able to run anymore, and his coaches knew it too, they knew he had to become more of a pocket quarterback.
But Kaepernick lacks two major assets to make that work.
WHAT CRUCIAL SKILLS Kaepernick LACKS TO BE AN NFL QUARTERBACK:
1.) He has very little consistent “touch”. He could throw long bombs, but anything else would more often get delivered, inaccurately, at high velocity. He had and has very little "touch" (throwing nuance) for a quarterback that could be engaged consistently.
2) He can't read a defense. Zolak said the book on him was to simply watch him when he got the ball and dropped back. Watch the stripe on his helmet. When he gets the ball snapped to him, he looks to the right or the left. Good quarterbacks like Brady, Rodgers and Brees look straight up the field when they get the ball. Kaepernick looks. He can't break the habit. And defensive backs got the book on him. The defensive coaches said: "Watch the helmet stripe."
In summary: Kaepernick cuts the field in half for the defenders. And when he can't get the first read, he is lost. He can't progress through his reads and what makes it even worse for him, he has no touch, so dumping it off is a real challenge. He is hot and inaccurate on those kinds of passes. When he goes to his safety valve (usually a running backing the flat) after his initial reads fail, that back is dependent on getting the ball delivered in a way that allows him to catch it in the simplest possible way so he can begin running, usually because someone is on him immediately. Often there are defenders nearby, so the quarterback may have to loft the ball a little to clear outstretched arms. Kaepernick can do neither of these, so the ball arrives at the safety valve running back too hot to catch, or the ball is batted down by a defensive player. That's Kaepernick the quarterback in a nutshell.
And there are more impediments for him:
NON PERFORMANCE REASONS Kaepernick IS NOT SUITED FOR AN NFL ROSTER SPOT, EVEN AS A BACKUP:
His off field BS does have an effect. Backups should be invisible, create no waves. Any team that signs Kapernick will have a circus on his hands. Not worth it.
Think about it from the perspective of a manager hiring a person. If you were going to hire someone, and they had a history of public conflicts and legal conflicts over personal issues that ended up in papers or in courts, would you hire him, even if he was better than some bland person with 90% of the skillset the problematic person offered? Of course not. You are going to hire the bland person who works hard, keeps his head down, and does his work, even if it is only 90% as good. That last 10% of lost ability is EASILY made up via "addition via subtraction".
Lastly, in my opinion, He is a douche. Wearing the Fidel shirt just confirmed for me what I already knew. I don't think he is a particularly bright guy, and to make it worse, he has a woman leading him willingly around to use him as a social justice tool. That is more important to him than football.
So, when the GM or Coach is told to evaluate Colin Kaepernick for their team they watch the film on him, look at his toxic personality and issues: 
Nope. Not worth it. He won't play again in this league, even if someone gets desperate. And it won't be because he is being blackballed.
It will be because, in today's NFL...he simply cannot play the game it is being played. He sucks.