We have rented a car at MIA airport after cruises each of the last two Januaries and will do so again next January (we're doing b2b 5 night cruises on the Magic this time, did b2b 3+4 last January). I have rented from National using free days earned from prior rentals so I only paid for taxes, fees, gas, and tolls. This next time, I have a one-day reservation for $59.20 plus taxes, fees, etc. for a total of about $70. I will likely rebook this using a free day credit since I only need one more rental to earn one and I will be renting a car for a trip we're doing in September.
The toll roads in Miami use toll-by-plate and the National/Alamo toll service fee adds $3.95 per day for each day when you have tolls charged. My charges for tolls getting out of the airport car rental facility to I95 northbound were a total of $6.15 including the service fee. I paid cash for another $2 in tolls on 528 and $3 in tolls on 417, taking I95 to 528 to 417 to WDW rather than taking the Florida turnpike. We usually stop for lunch near Vero Beach enroute and stop for groceries before checking into our DVC at the BW.
ETA: National runs a shuttle from the port to the car rental facility at MIA. If you have to take a shuttle to pick up the car in any case, the airport facility has the advantage of good selection of cars and ready access to the highway out of town. We always drop off at the Dolphin in WDW since we stay nearby and National/Alamo are there, but most of the major car rental operations have locations near WDW in the hotels near Disney Springs. Of course you might keep the car for your entire WDW stay and drop off at MCO prior to flying home as well.