In addition to any revenue that Qantas may or may not get, I think there's a sales psychology angle. Interestingly, it work both ways.
On the one hand, if you get the fee waived it feels like you're getting a bargain, so - as Mr H points out - it makes a partner proposition more attractive.
On the other hand, if you do pay the joining fee you've invested actual money, so it acts as an incentive to keep engaging with the program so you can get your money's worth.
