The reason he failed was that he wasn't a good enough player that they couldn't ignore him. If it was Cam Newton or Aaron Rodgers or Russel Wilson doing it, the result would have been different. Because the league could credibly discard Kapernick on the basis of him being a borderline backup caliber player, they did.
I honestly think that the primary motivation for most of the powers that were in the NFL at the time was the avoidance of controversy - "if we just get rid of the guy at the center of all this he'll fade away into obscurity and the story fades with him". That, obviously, did not work out very well.
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