Yes we have rented a jeep twice and a van once while in Cozumel. Just check the prices, some are very competitive and some are not. Usually at all the ports there are rental agencies close by. Just be cautious while driving in the downtown area as there are a lot of one way roads and lots of pedestrians on the streets.
We have rented a jeep for all day for as little as 90.00 for the day, plus the insurance and gas.
Have fun, you can not get lost, there is only one road that goes around the island, and most agencies will give you a map and show you how to get back to the port.