Or, you could get a guide book and rent a car when you get into port and go out and explore the island on your own. This is what we ended up doing and it was one of the best days during the trip...impossible to get lost. We stopped at a beach club and swam for a bit, stopped at the ruins at El Cedral, stopped at Punta sur (lighthouse, a few ruins), had lunch at Coconuts on the east side, stopped at the ruins at San Gervasio, returned the car, changed and then still had an hour and a half to shop in San Miguel. The car was about $75 w/insurance, gas etc.
I also would recommend getting a guidebook (Fodors) and then just renting a car. Hertz is right there at the ship terminal. However, the ruins on Cozumel aren't much to see, so you may want to spend your time elsewhere. This is where the guidebook would help a lot