Not having to deal with dragging bags around and waiting hours for a bus/ferry is well worth the extra $$ to fly direct for us.
For me it's usually around $150-200 a person difference (sometimes even more). That's worth it and I really don't mind the bag drag at all. The total wait time for transportation from CUN to Playa and then the ferry usually adds up to as much or less then what I'd be waiting for a connecting flight to Cozumel. I'd much rather be waiting for the ferry, sitting beachfront sipping a margarita then be connecting in another airport.
If I had a non-stop available to Cozumel then it would be a different story. I don't, but I do have 3 flights a day to Cancun from my preferred airport on my preferred airline. If I want a little less convenient of an airport and airlines where I won't get upgrades then I have at least a dozen non-stops a day to Cancun to choose from... and still none to Cozumel.