The toll road will knock hours off your trip as opposed to the alternative, and I recall they do take dollars, with the round trip somewhre around $56.00. There aren't many services along the way save for a somewhat clean tollway plaza in the middle and miles of jungle out the window. But the road itself is in excellent shape and knocking off the trip from Cancun airport in 4.5 hours should be a breeze.
As for Merida proper, we had no trouble getting into the city in broad daylight, but leaving at night seemed to hinder us quite a bit. A map might be a good investment, and if you live in Madison by chance, the University Book Store at Hilldale mall has an excellent map of the Yucatan with detail showing Merida and the ancient sites. I just bought one there this past Thursday and they had three or four remaining. Downtown location has them as well.
We took the First class ADO-GL bus from the bus station in Cancun to the First Class Bus station right across the street from the Fiesta Americana. There is a rental car place right next to the bus station by the way.
The bus took ride took about 4 hours. It was well worth the $25 or so each to let someone else do the driving while sleeping. The seats recline completely on these busses and are very comfortable.
The bus takes hwy 180 from Cancun to Merida. Highway 180 is just north of town in Cancun and not hard to find. The bus comes into town on hwy 180 which turns into calle 69. From there, it's a real rat's nest in the old city. Basically head into town towards 59 and 60 and then head north on calle 60. Odd streets are east-west and even streets are north-south. The Fiesta Americana is at the corner of Calle 60 and Colon. Calle 60 is one way south to north. Montejo Blvd runs paralel to Calle 60 and goes both ways. You can see this on Mapquest. Simply look for Merida, Yucatan MX