Last month I flew into JAX for a conference and drove to Disney for lunch (my partner forbade me from actually going into the parks without her).
It took about three hours. I was expecting about 2 hours so that last hour killed me. If you save a lot, not a bad idea to fly in there.
As far as car rentals go, I had gotten a great deal with National and it was very easy to get the car.
I wouldn't hesitate to fly in there myself if it was cheaper (I'd say if I saved about $100 or more, I would fly there).
However, it is more expensive for me to fly to JAX so that probably won't be happening.