If you are talking about getting from the airport to your WDW on-site resort and back to the airport on Disney's Magical Express, not all of those buses are accessible. You would make your arrangements for that when booking your DME rides. There is more information about that in the first post on the second page of the disABILITIES FAQs thread. That thread is near the top of this board or you can follow the link in my signature.
The buses, monorails and most of the boats that go from place to place on Disney property are wheelchair accessible as livndisney mentioned. You don't need my special arrangement to use them.
If you are staying off site, you will need to check with your resort directly, since the accessibility at off site places varies. If they provide shuttle service to guests, they also have to provide accessible shuttle service, but how to arrange it may vary from place to place.