First some geography help, and second some travel tips.
Merida, Mexico is not on the water, so a ferry can't go there. The place the ferry is most likely to dock is at the port of Progresso, which has a huge pier (6KM long). Progresso is about 45 minutes north of Merida. Merida is a really beautiful city.
How to get to Belize "overalnd" from Cancun -
1. Bus - take first-class - very comfortable and under $20.
2. Car and Driver - Call Menzies Travel in Corozal. 422-4725