That’s what’s so funny to me about this situation. He got to thinking he was hot stuff and that everyone would fall all over themselves trying to get him. So he opted out of his contract to become a free agent, only to discover nobody wanted him. If he hadn’t done that, he would still be playing.
NFL contracts are not guaranteed in most cases. The 49ers knew last season that they wanted to cut Kaepernick after last season and avoid paying out the rest of his contract.
However, since they knew they wanted to cut him after the season, this also meant that they could never let him play in a game and risk an injury ... because under the current collective bargaining agreement they would not be allowed to cut him if he had been injured in an NFL game. So their plan was to basically let him sit on the bench all year and pay him what they owed him for 2016, and he was never going to get into a game for even a single play.
He opted out of his contract during the season last year because he knew that his value to another NFL team for this (2017) season would be almost zero if he never played a single game in the NFL in 2016. By opting out of his contract, he gave the 49ers the option to play him last season without having to worry about getting stuck with him after the end of 2016 due to an injury. He got into a few games and put up some half-decent numbers, but as it turned out that didn't help him at all this year.