It's not politics, it's business - From FOX Sports
Kaepernick is going to get the same check for 2016 whether he’s on the roster or not, and while there was some thought as to whether it’d be more prudent for the 49ers to use his 53-man roster spot on another player, the team decided it might as well keep the guy it already paid around — he has experience and as far as emergency backup quarterbacks go, he’s not a bad option.
Kaepernick burned the 49ers last season after he injured his shoulder in the early part of the year and played through the injury until he was benched for poor play.
Kaepernick didn’t exactly engage in a rehabilitation plan that would get him back on the field immediately and he waited to have surgery on his shoulder, knowing that if he made it to April 1 and he wasn’t fully healthy, the 49ers would have to pick up the full $11.9 million he was owed in 2016.
Kaepernick had the NFLPA ready to pounce if push came to shove.
Kaepernick missed the first two games of the preseason recovering from that surgery, too, and by the time he played (poorly), the anthem controversy was full bore and the 49ers didn’t have much of a choice but to keep him — unless they wanted Jeff Driskel to be their backup quarterback.