I can only speak from Port Canaveral experience, but I love using the Disney Transportation as well as flying in the day before and staying at the MCO Hyatt.
I really like the convenience of leaving my luggage in the hotel room the morning of debarkation and having it "magically" reappear in my stateroom on the ship.
I also like the vintage cartoons playing on the bus on the way to the cruise (particularly if I am traveling with new cruisers - their excitement seeing the ship as we crest the last couple bridges to the port is priceless)
I also tend to do my best to be on one of the first buses leaving the airport in the morning. I have been lucky enough to be on buses that arrived before the port terminal was officially open to the public for the day and got to check in at an essentially empty terminal. The downside of that being the wait from check-in to boarding can seem like forever but it is fun watching the terminal fill up over the hours we wait.
I have also always used the Disney on board airline check in process. Again, the convenience of leaving my luggage just outside my stateroom and having it "magically" appear at baggage claim when I get home is awesome. No trying to find luggage at customs or dragging it behind use to the airport.
All in all, I think it is worth the extra cost just like I think a
Disney Cruise is worth the additional cost when compared to other alternatives out there. I can certainly understand saving money by choosing different options but I have yet to see any that provide the same level of convenience from my experience.