That's different for you guys; you probably have to retrieve and recheck your luggage in the US and go back through security, don't you? If not and it's only the time that's involved, I'd still pick the layover instead of having to schlep myself and all my equipaje from airport to cab to boat to cab to hotel.We take the bag drag any day over a layover (in the States). Coming from Canada it adds waaaaay too much time at the airport in Toronto to preclear US customs and, once you add this to the actual layover time, it's faster and usually much cheaper to fly in and out of CUN.
When I go to Cozumel it's usually for a couple of weeks, so I'm not in a hurry; a couple of extra hours between flights in a layover is no big deal. But of course DSFDF and YMMV.