I would imagine Paypal charges companies for using its services.
Games Workshop did, but FW is seperate an entirely seperate company (albeit one wholly owned by GW). As such, FW is responsible for running itself which means no subsidies from GW and that they have to turn a profit themselves. FW will be responsible for all it's own production costs, meaning it is paying for the books, not GW. And you don't maintain 40% profit increases by propping up loss making companies.