It's not as simple as that. While they do have $60M under the cap and have done absolutely nothing in FA so far, keeping him for the entire season will cost more than $11.9M. That's just the guaranteed portion of his salary.
His contract is as follows:
2016 Base Salary: $11.9M. This is the portion that is guaranteed if he's on the roster April 1.
Pro-rated Signing bonus: $2,465,753
Roster Bonus: $1,125,000. I don't know when this kicks in, but since everybody is talking about $11M guaranteed, it does not appear to be April 1. But at some point they'd have to pay him this portion as well.
Workout Bonus: $400,000. He's going to easily earn this as well since Chip Kelly has just said they will be working him out as soon as he reports.
Total Cap Hit for 2016: $15,890,753 if they keep him all season.
Dead-Cap Space if they cut him prior top April 1: $7,397,260 (mostly the unearned seasons of the pro-rated signing bonus).
It's just crazy to keep him, unless they plan on starting him. But, if they do that, what do they do with Blaine Gabbert who won the starting job last year by outplaying Kaepernick? I suppose Chip Kelly could be crazy enough to pay his backup $16M and his starter $6M but it's not going to make either QB happy.
And $12.3M is a lot to eat on a contract just to try and make the Broncos, Jets or Browns cough up a 2nd round pick when they are not going to do that. They reached agreement with the Browns but the Browns want Kaep to take $8M (backup money) to come in for a year until Jared Goff or Carson Wentz is ready and he doesn't want to do that. He wants to start.