I've taken 3 Disney cruises so far, and used different transportation each time.
First trip we booked a towncar service. Nice, but pricey.
Second trip we rented a car at the airport, used it for 3 nights at WDW, then drove to Port Canaveral and returned it. The car rental agency (I want to say it was Thrifty, but can't remember) had a shuttle to the port. Then, when we came back we did the process in reverse. It wasn't too bad, however the wait to rent a car after the cruise was ridiculous! A huge ship full of people descending on Port Canaveral at the same time meant a ton of people looking to rent at the same time. Long wait for the shuttle, long wait at the agency. And then they were all out of the car type we had reserved. Wound up with a convertible as that was all they had left. It worked out fine for my husband and I (though it was raining, so not too fun). However, what if we had been a family needing a minivan? Cheaper than using Disney transportation though, plus we got to use the car at WDW.
Third trip we rented a car at MCO, spent 2 nights at WDW, and then parked the rental at Cruise Parking of Port Canaveral. After the cruise we just took the parking lot's shuttle back to the car (very short wait), and were on our way. Only about $40 more than Disney transport, got to use the car at WDW, and also used the car to store items we needed at WDW but not on the cruise (like car seats).
This coming trip we plan to rent a car and park it during the cruise! Good luck with whatever you decide!