The time really varies based on a number of factors. The line at the ME counter can be long, I've taken from 5 to 15 minutes to go through the line. The bus line can also be long, I've waited up to 40 minutes this past January when no busses were available, other times 5-10 minutes. ME can stop at up to 3 hotels when they are going to Disney. In general a time from getting to the counter to getting to the resort will be between 1 - 1 1/2 hours most of the time, maybe up to 2 hours at really busy times. Magical Express shines at getting you back to the airport. They do pick you up 2 hours before your flight time but the convience of walking up to security and just going through that is well worth it, no bags to check.
My average time in renting a car is not much different, by the time you pick up your luggage, go to the rental counter and get everything into the car and then off to the resort it takes about the same time. The big thing is that ME saves you lots of money. Cab fare is $50 each way, limos are $100 or so and car rentals would be more.