There's a few ways you can get to Cozumel - fly directly to the island's airport from the USA, fly in to Cancun and take a puddle jumper there or fly to Cancun, take a bus/shuttle/cab to Playa del Carmen and then a ferry from there to Cozumel, aka the "bag and drag".
Flying directly to Cozumel isn't a great option for West coasters as it involves either a red eye flight or an overnight layover in Houston, Dallas or Atlanta. Since there's a couple of non-stop flights from SFO to CUN, the other 2 options are far more appealing. We looked into the short flight from CUN to CZM but the amount of time it took for the terminal transfer and then waiting for the often delayed flights was more than it took for the bag and drag. That's why we opted for the latter this time.
Our flight landed in Cancun at about 4:30PM and we were hoping to make it to the Aldora dive shop in Cozumel before 7PM to check in and drop off our gear for the next morning dives. This meant that we didn't have much wiggle room for the bag and drag and needed everything to go pretty smoothly to make it there in time. Even though we got the red light at customs, we were out and in a shared ride shuttle in less than 30min. Even better, we actually ended up being the only people in it and were driven straight to the PDC ferry terminal. Woohoo! This took about 45min and we got there just in time to get on the 6PM ferry to Cozumel. A gentle ride later, we were finally on the island and just in time to get to the Aldora dive shop. Aaaaah, it's awesome when everything clicks.
Why the rush to get checked in that evening? Not doing so would have meant waking up an hour earlier the next morning - I was super glad to not have to do that.
Since we were also staying at the Aldora villa, they arranged for a transfer from the dive shop to the villa which is at the far north end of town, near the airport. Chris and Chris at the Villa are awesome and gave us truck rides into the city and even cab money to get back. Sweet!
Strangely enough, we ate burgers at Rock n Java for dinner our first night in Mexico.