Below we have a number of options to get from the Cancun Airport to Isla Mujeres.
You can always take a taxi from the airport and there will be many willing drivers outside of the airport. This can sometimes be overwhelming with everyone wanting to help you at once. Their prices can vary considerably, but offer the convenience of just getting in and going. Always ask the price, before you get in the cab!
AGI Tours offers a transfer service from the Cancun airport. They hold a sign with your name, as soon as you exit the airport. This is a link to their website, and pricing: http://www.agitours.com/transfers.HTML You'll be transferring to Puerto Juarez to get to Isla Mujeres. We have had great personal experience with them and if you're late, they'll wait.
A very economical way of getting to the island is to take the ADO bus. This is a bus transfer from the Cancun airport, to the bus station in down town Cancun. (It was originally made for airport employees to get to and from the downtown for a reasonable price. Now it is quite popular among budget travelers.) Tickets are just 35 pesos a person and leave every half hour. Once at the bus station, it's a very reasonable cab fair to go to Puerto Juarez. It's a couple transfers to get to the ferry, but this is a very economical way of getting to the island.
Once at Puerto Juarez, buy a one way ticket to Isla Mujeres. There are departures from Cancun to Isla Mujeres every half-hour (on the half-hour) from 5:30AM to 8:00PM, then ferries at 9:00PM, 10:00PM, 11:00PM, and 12:00AM. Once on Isla, the taxi stand is to your left. You can tell the driver to go to Hotel Las Palmas or the 'Mercado Municipal'. For directions to walk to us for the first time, please email us with your request. We will be adding a map with directions to our site soon.