Here's the official wording from Disney from the original Magical Express FAQ:
Will Disneys Magical Express continue on a complimentary basis after the Happiest Celebration On Earth has concluded?
While no determination has been made, our focus right now is the successful launch of Disneys Magical Express as a great new benefit for our guests.
My guess is that Disney's Magical Express will continue to be complimentary.
Disney isn't offering DME on a complimentary basis during the Celebration just to be nice.
The business reasons for Disney's Magical Express are to increase the perceived value of Disney-operated on-site lodging (to increase occupancy and to decrease the need for big discounts) and to discourage guests from having rental cars (which make it easy for guests to spend money off-site). Those business reasons will be just as valid in 2007 and beyond as they are in 2005 and 2006.
Sure, Disney could get some revenue by charging a fee for DME, but it would also discourage guests from using DME. The operating costs for DME would not go down appreciably, but the motorcoaches would have more empty seats, on-site lodging yields would be likely to go down, and more guests would spend money on off-site dining, shopping, and attractions.
Of course, I could be wrong (but in this case, I don't think so).