Parking is free for resort guests.
I always have my car with me, so I do a mix of Disney transportation and my own driving.
If I want to be at EP, AK or HS before rope drop, I drive. Rope drop at MK, take Disney transportation.
If I'm going to enjoy adult beverages, I take Disney transportation.
If I'm going to close down a park and not hop to another park, I drive. It's a bit of a toss-up on this one for MK because the buses are right at the MK gate. But for all the rest, I prefer sitting in an air conditioned car while battling the exiting crowds.
If I'm not going at rope drop or not closing down a park, I check to see how crowded the bus lines are and then decide. If the bus line isn't long, I'll usually opt for Disney Transport.
If it was a choice between a rental car and Disney Transport, Disney Transport is fine and I wouldn't pay the extra for a rental car.