Despite the numerous issues that Formula One has, Bernie has created a system that is impossible to turn down. And once you decide to play his game, you are locked into contracts that are punishing if you break them. Although the tracks are subject to insane fees, all studies indicate that hosting a Formula One event confers tremendous economic benefits to the community in the form of increased tourism and positive world-wide exposure.
Bernie is the goose that lays the golden eggs. The teams and others involved know this. Because of what he has created, a lot of people that have been in Formula One for a long time are very rich people. Two examples are Sir Frank Williams, and Ron Dennis. They have their differences with Bernie at times, but they know that without him they would not be the very rich men they are today.
There are people and organizations that have decided that they do not want to play in Bernie's sandbox. For instance, when Bernie attempted to hike the fees for Indianapolis Speedway, Tony George basically told him to stuff it. Indy makes a lot of money from other events, it would not be the end of the world for IMS if Formula One was not there. And when Montoya got sacked from McLaren, he could have easily found a ride in another team. But he chose to go elsewhere, away from the crazy politics and insanity.
But basically, if you are involved in Formula One, you are locked into contracts impossible to break, and once you burn that bridge, you can never return.