I imagine (but maybe wrong) that things such as wages, fuel, bus station fees are all included within the bid as 'operating costs' - with a bit extra added to the bid, counting as profit.

Or

The bid is 'discounted', to take into account the bus station fees. So wages, fuel and profit are calculated, with the bus station fees then deducted.

Unless anyone can come up with the official answer or an alternative.

Edit: Possibly looking like one of these simple forumlae C + F + P = Bid or C + P - F = Bid

* C = Operating costs
* F = Bus station fees
* P = Profit

Some of the bigger operators may take a loss on the fees, depending on the service and discount them from the bid.