I have to agree with the above poster that said bus to MK, rental car everywhere else. Disney's bus transportation drops you off practically at the front gates of the MK, whereas if you drive, you still have to transfer to the ferry or monorail; it will take you an additional 10 minutes or so if you choose to drive.
That said, I only use bus transportation to the MK. I drive everywhere else. I hate being dependant on Disney transportation, and having a rental car is so much more convenient, especially going to Downtown Disney. Plus, having a rental car gives you the freedom to go off-site, if you need to go grocery shopping or simply want to go shopping at the outlets.