Kaepernick turned down the AAF because he had a collusion suit going against the NFL, and the huge drop-off in talent in the AAF would suggest he's accepted his unworthiness for the major leagues. The $20 million was asserting his worth. He knew the AAF couldn't come close.
The AAF also went heavy after Tim Tebow and Johnny Manziel. You can guess what those three quarterbacks have in common. They also turned down the AAF.
It's a good question about Patrick Mahomes, but to be accurate Patrick Mahomes would have to follow up his impressive debut by leading the Chiefs to the Super Bowl next season, and losing a nail-biter. Then Mahomes would have to lead the Chiefs to the AFC Championship the season after that, Then he would come down to Earth a bit the season after that. Then the Chiefs would fire Andy Reid in a front office squabble and lose most of their best talent. Then Mahomes would look like a really average quarterback and all the haters would come out. The inexperienced new coach would then start Blaine Gabbert over Patrick Mahomes, and Patrick Mahomes would fade out of the picture until he started kneeling during the national anthem. Then there would be a huge outcry. Then the coaches would realize that Patrick Mahomes was still better than Blaine Gabbert and let Mahomes finish the regular season, where he actually performs pretty well, all things considered. Then Mahomes would be released to pursue another team, but no one would hire him because of the controversy. But Blaine Gabbert would never be without an NFL contract because apparently his talent outweighs his baggage.