I think the issues were: (1) For the the NFL's organized workout to take place he was being required to sign a standard release of liability waiver for any injury that may occur
but his waiver was appended at the last minute to include language in which he would relinquish any right to sue the NFL in the future (release of
all liability) for whatever might result from the workout (for instance, continued lack of employment). He refused to sign that waiver. And (2) The official NFL workout would have been closed to all media and Kaepernick's team felt there was a high likelihood that the results of the workout could be spun in a manner that disparaged him. All 30 teams were going to have a representative there so he was vastly outnumbered if it became a game of he-said/he-said about how ready he looked to play an NFL game next Sunday. These are the same teams who supposedly colluded to keep him out of the league, after all.
Full disclosure: I enjoyed watching him play for San Francisco and I think, despite his flaws as a pocket passer, Kaepernick is talented enough to be playing in the NFL right now. I also think the NFL botched the whole anthem kneeling story in their haste to appease a fanbase that historically skews conservative. I don't know that any collusion actually took place (that's hard to prove) and I also don't expect Colin to ever play in the NFL again. Partially because of the media footprint which now follows him around (is a second or third string QB who won't see the field much without an injury worth that kind of trouble?), partially because teams are always more willing to take a flier on young unproven talent than a vet fighting to keep their spot in the league, and partially because he played his last two seasons in the league for post-Harbaugh Niners teams which were absolutely gutted by injuries/defections/early retirement and were so bad that any QB in the league would have looked awful leading them. The tape is the tape though and it can't be unseen. I'm always going to remember him for that
time he ran for 181 yards against the Packers in the playoffs and for being brave enough to use his celebrity as a starting QB in the NFL to bring attention to a cause he believed in, to the detriment of his professional future. Whether you agree with his cause or not, the guy is not a villain.