Yes.
Magical Express provides complimentary transportation from Orlando International to your WDW resort on your check-in date. It doesn't matter if you arrive at the airport by air, by car, by taxi cab, by hotel or rental car shuttle or by taking the elevator and escalators from your room at the MCO Hyatt.
Don't use the yellow luggage tags. After you check out from your hotel, check in at the Magical Express Welcome Center. The motorcoach has a luggage hold, and the driver will store and retrieve your luggage (in which case a tip is customary). Also, you won't get the free "magical" luggage delivery to your room, but if you want luggage assistance, a bellman can help you (in which case a tip is customary).
When this subject was come up previously, some posts have suggested giving fake flight information to Disney. However, there's really no reason to lie to Disney.
I recently called Magical Express at 866-599-0951 because we're going to return a rental car at MCO (after spending a few days in Southern Florida) on the day that we check in at WDW. The woman at Magical Express explained that we are entitled to use Magical Express, and that she would simply make a Magical Express reservation without flight information.