One option might be to find a car rental company that has offices in Cancun and Chetumal -- Europcar is one I know, only because they are one of the two companies that allow cars into Belize. There's usually a fee for not returning the car to the point of origin, but maybe you can talk to them and see what they can do -- maybe you can leave the car with them and get it again when you head back to Cancun.
From Chetumal, there are 2 daily water taxis to Ambergris Caye, and they continue to Caye Caulker. Both depart Chetumal in the afternoon (3:00 & 3:30 pm). The water taxis return to Chetumal in the early morning.
You can find links to the water taxi websites on this site...http://belizebus.wordpress.com/
If you decide to terminate your car rental at Chetumal, you could return to Cancun on an ADO express bus.