For the same reason why AB lost his job despite still being one of the better WR's. Even is you are better than others, the moment you are more of a distraction than you are worth, your gone. Kapernick was fastly becoming the latest Jim McMahon/Doug Flutie/RG3. All had fantastic few years but quickly lost what made them special and became back ups. People don't think of Kapernick that way because he forced out so people don't have that image of him sitting the bench. They view him as a hero. Which is fine, but that still don't change reality.
I mean...our point was that players very famously face consequences for their public political speech, therefore, coaches should be held to the same standard. You seem to be agreeing with us by saying that Kaepernick was sent packing by the entire NFL because he "became a distraction" and not because he wasn't better than at least half of the QBs in the league.