1) You tell them when your flight is, and they tell you when it's convenient for them to pick you up. Since it's absolutely in their interest to get you to the airport on time, I've found that they pick me up some six hours before my flight leaves. I spend the next two hours shuttling all over the damn place picking up other passengers, and then I arrive at the airport a good three or so hours before my flight leaves.
2) Their drivers, almost uniformly, drive like maniacs. On a recent SuperShuttle trip, our driver hit a parked car, a parked motorcycle, and sheered a retaining wall. We passengers all decided it was best to close our eyes; we wished each other luck as we were dropped off at our destinations.
3) Do Not Pay Ahead Of Time. If their scheduling gets screwed up and you end up having to ditch your reservation because of their error, you want to be able to cut your losses and not go through a complaint process. It's cheap; pay in cash.
4) Having a door-to-airport service does not mean you can close your eyes and have everything taken care of for you. You need to know how long your trip will/should take, and how long before take-off your airline's check-in service closes.
5) While navigating SuperShuttle's phone service is a first-class pain-in-the-ass, and while dispatchers have--just today!--lied to me, once I met the driver, he gave me a straight, honest answer to my questions ("seriously, how many people are you picking up before you go to the airport?"), and once I reached the woman assigned to answer the phone calls of pissed-off customers, she dealt with me professionally and credited my friend's credit card. So: not dishonest, but caveat f'ing emptor.