I'd rather they charge a small fee NOW if that's what it takes for Disney to be able to process the baggage for non-participating airlines like SW.
I agree with Horace, if Disney thinks Magical Express is reducing the number of car rentals and towncar grocery stops it'll either be free or cheap. If too many people use it for free luggage transfers, either skipping the bus or having some family members take the bus, Disney will be more likely to charge the full cost of the service.