The only options of which I'm aware are:
Take a flight that terminates in Cozumel, whether it connects somewhere on the way or not
or
Take a flight that terminates in Cancún
then
Fly on Mayair to Cozumel
or
Get to Playa del Carmen (by bus, taxi, or chartered transport van) and take the ferry
The first option is preferable when schedules make it possible and when it's not excessively expensive. There are no direct flights to Cozumel from my part of the world so, no matter what, I'll be making some sort of connection somewhere.
You can do the bus/ferry for about USD$25 per person each way, and for large groups a bit less per person (because a chartered van can end up being less per person), so I will happily pay $50 per person more to fly into Cozumel since that's break-even without even accounting for any other issues. The bus takes about an hour and the ferry about 40 minutes. It's theoretically possible to get from the airport to the island in 2 hours, but that requires optimal timing and a fair amount of luck.
You can fly Mayair for under $40 each way if you do it right, but as the original post points out excess baggage is very expensive. They weigh both carry-on and check-through and "excess" is anything over 20 kilos, so for divers with gear this is often not a good option. The flight takes about 20 minutes and flights are roughly every 2 hours.
As much as I prefer to get off the plane and be in Cozumel, it's not always practical. For example, on Friday I need to be at a government office during the morning and the earliest flights to Cozumel I can find land late enough in the morning that a slow immigration or customs line will make my trip useless. I can get a flight to Cancún that lands at 0748, which even with immigration, customs, bus, and ferry should easily have me on the island and at the office before noon. Depending upon how long lines take, I'll likely be able to get to the island not much later than than if I took the 1000 Mayair flight.
The "bag drag" is really not at all difficult even if you have a lot of luggage. The ADO buses are not far outside each terminal and one can get an inexpensive porter to get luggage to the bus. In Playa del Carmen the bus station is about 3 blocks from the ferry landing and one can get a triciclero to pedal luggage there for a few bucks. The bus is comfortable and the ferry is sort of fun. Use Ron Lee's excellent walk-through for every step in the process. Note that although a post above referred to the bus being just outside Terminal 3, which it is, it's also just outside Terminal 2 if your flight lands there - there's no reason to try to get from one terminal to another to catch the bus.
