For information on flying with pets see: www.petflight.com
If you choose to stay at a Disney hotel, you can also book Disney's Magical Express, just mention it when booking your room. This free shuttle service will take you from the Orlando airport directly to your resort. Disney will send you special luggage tags so that they can claim your luggage. Once your room is ready, they will place your luggage in your room.
When you depart, Disney's magical express will take you from your resort back to the Orlando airport. Simply call the day before to schedule a time to be picked up. If you are flying on American, Continental, Delta, Song, JetBlue, Northwest, United, or TED, you can check in for you flight, get your boarding pass, and check your luggage at your resort.