Yes, in the end they did end up paying the reported $40 million fee, but that was after they tried to re-insert the race into the calendar. With the initial cancellation Bernie stated he would wave the fee for this year as a gesture of good will, but then they tried to re-insert the race later in the year and he wasn't so generous the second time around. This is what led to my comment about Bernie being between a rock and his bank balance.
The way a race is contracted is fairly strange in the wold of sport, but the basics are something like this :-
1) Venue says it is interested in holding a GP, they negotiate with Bernie to get a spot on the calendar (something which Bernie himself doesn't have the power to grant) and agree a payment of varying size to FOM.
2) Bernie is then contracted to provide a full grid of cars (as defined in the current sporting regs/concorde agreement).
3) The venue is under obligation to aquire the appropriate sign off by the FIA, provide all the facilities, marshalls, and is allowed to sell tickets to the GP.
4) Bernie gets to sell all the advertising at the venue for the GP weekend (and keep the money).
5) Bernie is allowed to sell the TV rights to the GP weekend (and keep the money)
6) All costs for hosting the GP fall to the venue (and they get to keep any money that is left over after that from the ticket sales).
So, if Bernie calls off the race, he is contracturally obliged to provide a full grid of cars which is not showing up, hence it costing him money. If the FIA call off the race Bernie is still contracturally obliged to provide a full grid of cars, costing him money. If the teams call off the race then Bernie is still under obligation, but he has a fall guy to take it out on (the teams). If the venue calls off the race then they still have to pay the race fee, plus compensation to Bernie for all his costs.
Guess which of the two options Bernie wants to happen? The venue has made it clear that they will hold the race if everyone tuns up, so he has pushed it to the teams to say they are not going, Bernie doesn't lose out and the teams lower their bank balances in order to have an extra weekend off.