$50 will just about cover the round-trip costs of the bus and ferry, so saving $50 going into CUN is not a deal, that's break-even. $50 more to go straight into and out of CZM is an absolute no-brainer if other factors are equal (such as connections).
I can't imagine any realistic circumstances under which flying into CUN would get you to a hotel or house in Cozumel faster than flying into CZM would.
For $50 more, I agree with you. Last few years it has been closer to $200 more to fly into CZM.
The overall trip time won't be faster but it's easy to get to your destination earlier in the day doing the bag drag. There is one United flight there for me, arriving around 3:30pm. There are 7 or 8 flights into CUN arriving as early as 10am. Add 3 hours and I'm still there in time for an afternoon shore dive or enough pool time to get sunburned.