We prefer to drive ourselves. It's almost always a shorter trip by car than by bus, in my experience. We usually stay at a value resort, so our car is parked reasonably close to our room. We get dressed in the morning, pack up our breakfast, hop in the car, and eat on the way to the park. Saves a LOT of time (and we eat more healthily)! On one trip, we compared the time it took at park closing to get from both DHS and Epcot by splitting up. My sister and I parted at the exit to the park; she (and her kids) headed for the bus lines, and my daughter and I headed for the parking lot trams. I was ALWAYS back at our hotel (POP) before she was- and had had time to shower before she walked in the door. At the end of a long day, the last thing I want is to stand in line for a bus, then stand on the bus (packed in like sardines), then walk from the bus stop to my room. As far as going to MK, yes, you have to park at the TTC and then cross the Lagoon to get to MK, but that's part of the fun. You ride the tram in from the parking lot and then take either the ferry or the monorail to get to MK. Ferry and monorail riding are NOT part of our everyday lives- it's FUN to ride the monorail at Disney!
If you are traveling with little kids, having your own car is a bonus because that stroller will be in your trunk. It's a pain to have to manage small children and a folded stroller on a packed bus (usually no seats available)- and imagine at night, if that child is asleep in your arms, and you have to deal with holding a sleeping kid, balancing yourself and child, and deal with stroller, other kids, bags, etc. SO much easier to throw everything into your trunk, strap the kids into their car seats, and drive back to your hotel. (We always had DD's car seat in the airplane with us, then lugged it around in a special bag with shoulder carrying strap, so not a big hassle to fly/travel with the car seat).
I did the who Disney Transport back in 2007 and well, lets just say I don't want to do it again.
