From Travel weekly-
DISNEY CRUISE LINE will begin offering passengers "onboard airline check-in" this season, a service that enables its qualified guests to check-in for post-cruise flights from Orlando while onboard the Disney Magic or Disney Wonder. Besides checking in from the ship, guests' luggage will be transported directly from the ship to their flight on the seven participating airlines: AirTran, Alaska, American, Continental, Delta, Northwest and United. To participate, passengers will have to complete preregistration information from Orlando Airport or a Disney Cruise Line Hospitality Desk at the Disney World Resort and turn it in during cruise check-in at Port Canaveral.
This is the same service that Disney on-site resorts currently offer.