Just thought I'd post this as some of you have probably wondered the same thing.
I was looking for a return flight Perth to Bali using my FF points the Tax on the flight was $185. The flight is actually a jetstar flight with a qantas flight number. If I compare the exact same flight on the jetstar website the cost of the Tax is $75 so aprox $110 cheaper than the tax been charged on the FF booking.
I have rang qantas and they said that the reason is that if you book through the FF program you are booking a flight with a qantas flight number and all qantas flights are subject to fuel surcharges (even if it's a Jet Star flight). Apparantly Jetstar either choose not to charge a fuel surcharge or it is inbuilt in the ticket price.
Her advise was that you get more benefit from your points if you use them on qantas routes as opposed to Jetstar or other airline routes.
I don't agree with it but at least I know why now.