Kaepernick's starting record last four years:
2013 12-4
2014 8-8
2015 2-6
2016 1-10
He had early success because he was a good running QB, and was okay at hitting the first read. Harbaugh took advantage of that. When Harbaugh left, his success went down every year, as teams figured him out: cover the first read and contain him on the scramble.
Nothing in the press happens organically. ESPN decided to push the protests, and started doing a weekly "who's kneeling for the anthem" segment. The protests blew up in their face, and NFL ratings dropped. Some of the drop was from over saturation and that third tier crappy games were getting televised nationwide, but there was a legitimate fan backlash against the protests.
Kaepernick's numbers had gone down every year, and no one wanted to sign him as a starter. The problem with having a guy who doesn't fit the mold as a backup is you want your backup to come in and execute a game plan. You don't fit your offense to what a backup QB can do. Vince Young and Tim Tebow both had the same problem trying to catch on with another team after getting released by their first teams, even though Tebow had a winning record his only year as a starter, and Young's record was .500 in his last year that he started eight games.
Kaepernick had the additional problem that he was famous as a celebrity, not because of what he'd done on the field. Without the anthem protests, he's about as relevant as Shaun King, who quarterbacked Tampa Bay to an NFC championship game and lost.
Was Kaepernick shut out over collusion? I dunno. I do know that if I was running a franchise and needed a backup quarterback, I wouldn't look at him, because he would immediately become a distraction from winning games.