We always fly and use the transportation system. The only time we've had problems was when staying at POR we took the boat to DTD, then it stormed and we had to take the bus back. That was the nightmare bus trip....it took over an hour because of the storm.

I think if you are used to that kind of transport at home, you will be fine with the bus system. If not, and you are used to driving yourself whereever you want to go when you want to go, then rent a car.