The bus trip is about 5.5 hours so you can't make it to Chetumal in time for the water taxi on the same day.
This is how I do the trip from Cancun airport to Belize…
From Cancun airport to Playa del Carmen, there is an approximately hourly ADO Riviera airport shuttle bus (check the ticketbus site for departure times and fares). Tickets are sold at a counter in the airport just after exiting customs, or from the ticket seller where the bus is parked. To get to the bus, go out of the airport terminal, turn right and keep going to the other end of the terminal. The bus trip is about 1 hour and costs MX$106 (as at February 2010).
The airport shuttle bus arrives in Playa del Carmen at the bus terminal at the corner of Quinta Avenida and Avenida Juarez (5th Avenue and Juarez Avenue). Stay a night in Playa.
The next day, get a taxi (MX$15 to $20) or walk to the other bus terminal (Terminal Alterna) at Avenida 20 and Calle 12, where the bus departs to Chetumal. Here’s a link to a map of Playa del Carmen showing the location of the two bus terminals:http://www.travelyucatan.com/playa_del_carmen_mexico_hotel_map-a.php
From Playa del Carmen, ADO express buses to Chetumal depart at 0025, 0150, 0620, 0920, 1050, 1150, 1320, 1435, 1515, 1635, 1835, 1935, 2120 & 2358 (and there are a few ADO GL and OCC buses for a bit more money). The trip takes about 4.5 hours and costs MX$226 for Primera Class (as at December 2009). Check the ticketbus site for up to date schedules and fares.
The bus arrives at the ADO bus terminal in Chetumal. Get a taxi to the water taxi.
Another option for getting from Cancun airport to Chetumal is to get a bus or taxi from the airport to the bus terminal in Cancun city. From there, get an express bus to Chetumal. Cancun airport is located south of Cancun and north of Playa del Carmen, so this means first travelling north to Cancun, then getting a bus back south, but it avoids the bus terminal change in Playa.
You could stay in Cancun (there are some low budget but good hotels near the bus terminal), or you could get to Chetumal on the same day and stay a night there.
Schedules & fares can change anytime; check for updates at:https://www.ticketbus.com.mxhttp://www.adogl.com.mx/en/index.htm
Note 1: MX$ is Mexican pesos. On the Mexican bus websites, just the dollar sign is used to represent pesos.
Note 2: The ADO express buses have very good air-conditioning; dress warmly.
Note 3: If you get an error message when you click the link for Ticketbus, try this:
1. Look at the address bar; the URL ishttps://www.ticketbus.com.mx/ticketbus/inicio.jsp
2. Use the backspace to delete the last bit (/ticketbus/inicio.jsp), so that only https://www.ticketbus.com.mx
3. Hit ENTER and you should get the site.
More information & links here:http://belizebus.wordpress.com/