As I understand it the RFDS is a not for profit organisation. However the government subsidises all the wages costs and fuel of the organisation paying fair market rates to nurses/doctors/pilots and administration roles.
The fund raising they conduct helps in the purchase and fit out of the aircraft.
Rather than critise the wages that the doctors earn, either get qualifications and go to uni for 7 years, go thru internships etc on poor money before you start to earn that sort of money.
They get paid what they worth and what they as a profession 'value' their labour and skills at, like any other profession where high wages are on offer.