It depends on which airline. Frontier flies there from a lot of cities, including their hub in Denver. Spirit from Ft. Lauderdale. Continental/United has the only direct flights to Merida, from Houston. But in the odd way legacy airlines work, it is sometimes cheaper to go through Houston from elsewhere than to go there from the hub.

Lots of charter airlines fly to Cancun of course, like USA3000. I once got a flight from Nashville to Cancun on one of those for $99 each way.