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They really need to get a handle on this ASAP. I REALLY don’t want to have to cancel my Cozumel vacation plans!
Here's the US State Department website. I don't see anything about ferry usage.
Mexico Travel Advisory
"There are no restrictions on U.S. government employees for travel in Quintana Roo state, which includes tourist areas such as: Cancun, Cozumel, Playa del Carmen, Tulum, and the Riviera Maya."
This warning came from the US embassy in Mexico as a security alert, not a travel advisory. I received the email because of enrollment in the Smart traveler enrollment program (step). I don’t know anything else besides this email.
All I know is that the State Department website is not limiting government employee travel in the region.