We know of people who used the ferry through a ship's tour. The sea crossing became rough and service back to Cozumel was suspended for the day. They got flown (on the cruiseline nickel) to the next port of call--Miami to disembark.
We did this ferry to tour Tulum--fabulous, definitely memorable and worth seeing. However I would never try to do this again without being in a mainland port. The ferry ride is a couple hour round trip and was such and adventure in motion sickness (people throwing up right in front of their own seat) and we had a relatively calm day. Too much transportation, not enough historic ruins.