We drive, for several reasons. One, we have a 3 y/o and a stroller.
Second, we go pretty early in the AM, so we usually just breeze in and park within easy walking distance of whichever entrance we're going to. No trammin'.
Third, we often do early theme park, back to the resort for lunch/nap/pool/whatever, and then back to a theme park in the late afternoon. Making two round trips is MUCH quicker with a car than by bus.
Additional factors are that we know when the car leaves the resort, and we know when the car leaves the theme park, so there is no waiting or uncertainty. We are also assured of comfortable seats and no obnoxious people other than ourselves.
Especially with a tired 3 year old, it is good to just walk out of the park and drive home without any additional drama in your life. Of all the benefits of driving, I think the easy-out is the biggest plus for us.
On the other hand, I have a lot of friends who bus everywhere and wouldn't do it any other way. Although you'll hear an occasional anecdote about the bus trip from Hell, I think most people would agree the system works pretty well.