A lot of factors go into deciding what to pay someone.
You look at Matt Ryan of the Atlanta Falcons. His contract is for $103.75 million over five years ($20.75 million average), with $42 million guaranteed.
Colin Kaepernick $126 million over six years ($21 million average), with $61 million guaranteed.
Jay Cutler, Bears $126.7 million over seven years ($18.1 million average), with $54 million guaranteed
Peyton Manning, Broncos $96 million over five years ($19.2 million average), with $58 million guaranteed.
The first thing an owner is aware of is how much money he is making off of the team and what his share is of the TV market. The NFL is over a $9 Billion enterprise.
Secondly you look at what a player's impact has been on the team and compare that to any (available) potential replacements. Winning division titles, performance in playoffs, and Superbowl appearances/wins
Lastly you look at what stage they're in concerning their career and how much (the community) embraces them. After all it's the locals who buy the season tickets.
No player has ever earned more money than the owner of the team. Salaries are based upon the owner's "perceived" value and the marketplace. This deals locks Colin Kaepernick up through what most likely will be his prime years if he stays healthy. Younger players also tend to recover better from injury than older ones. In the little bit of time he has been a starter he's out performed both Matt Ryan and Jay Cutler in my opinion. Peyton Manning is still doing well considering his time in the league. Nonetheless everyone holds their breath each time he's sacked.
However if we were strictly going by performance by (active) QBs who've won Superbowls then the top paid QB would be Tom Brady who has won 3 times and has appeared in 5 of them. Tom is not even in the top 10 paid quarterbacks! or is he? Brady's base salary for the 2013 season is $1 million, followed by a $2 million base salary in 2014. The ($30 million signing bonus) and salaries for the next two seasons are fully guaranteed.
Timing is also a key factor. Some of the past greats can only speculate how much they'd make in today's market. Joe Montana would get a percentage of the team!