Depending on his performance the pilot earns money with each flight. On FSAirlines an airline can set a percentage of the income which goes to the pilot. If the profit from a flight is negative the pilot will get nothing.
After adding all the costs and incomes from a flight together the pilot salary is applied (without multiplier). If for example a flight makes 100,000v$ profit and the airline pays a pilot 15%, you will get 15,000v$ from that flight. The remaining 85,000v$ are multiplied by the multiplier then and added to the VA's account.
Editing the pilot salary
The pilot salary can be changed by the CEO or other pilots who have the right to edit VA settings. On the Virtual Airline Overview page under edit VA settings they can set a standard percentage and add custom rates to certain ranks.