The NBA players are payed what the team owners and GM's agreed to pay them in when they signed their contract. They are payed those ridiculous salaries because of the marketability of the league in the same way in which colleges recruit talented high school athletes from around the country in order to have a product on either the football field, basketball court, etc. that in turn maximizes the school's chances of winning (and also making as much money off of ticket-sales as possible). Any other cash that a college or university is making comes from either state taxes, or other forms of funding including student tuition, etc.
Just look at Dwyane Wade; he attended Marquette University and has already won a championship in his young career with the Miami Heat. If you don't think that the Miami Heat are a marketable franchise this season then you are probably crazy, and if you don't support the fact that NBA GM's are willing to pay top dollar for the best possible athletes to represent their franchise on the court then just don't watch the games.
As far as what the commissioner gets payed, I could care less as long as he isn't trying to dictate to the GM's how much they ought to pay their players.