The only plus side to the transportation to Disney is the fact that you do not have to drive yourself, pay for parking, find parking, then walk back to the parking lot and back. Where as if you have a bus, or something, you're waiting for that transportation to arrive and that's all the "waiting", or time consumption you really have besides the drive. For some people, including myself, that is good enough, even if there might be a longer wait, especially when you're happy you do not have to drive through construction, finding areas to park, and what not.
However, I find Universal is much better with transportation (and I guess others agree too), as for the most part, if you do not want to wait for transportation, things are at a reasonable walking distance. I especially like how close HR is to Universal. However, of course Universal is going to be better with that, as it's a smaller resort in comparison to Disney. Also, the bonus of HE is great too now that we have that, as it's not only a ride, but another way (potentially shorter way) to get to the park (if the wait time is reasonable).