I think a lot of people remember the situation as something like "he was a pretty good QB on a Superbowl team, then he started protesting and was blackballed from the league".
In reality, he was good in 2012 and 2013, struggled in 2014, lost his starting job in 2015 to Blaine Gabbert, then had shoulder surgery, then started protesting, then regained his starting job a few games into the season in 2016 during which the 49ers went 1-10. The 49ers then hired Kyle Shanahan, who wanted to run a completely different system and didn't think CK was a good fit, so they cut him.
The problems with him getting another job were that 1) you have to run a specific style of play for him to fit, 2) he's a backup QB, so he would need to go to one of the few teams that plays his style, and 3) is it worth going through the media circus for a backup/lower-tier starter?
If you have a pile of applicants and they are all pretty average, but one is controversial on top of being average, do you choose that person? Of course not. It would probably be worth it if he was really good, but that's just not the case in this situation.