Another update: Ferries from Florida not a priority for Cuban government (Tampa Bay Times, May 23, 2017):
[T]wo years to the month since ferries were federally licensed to sail to the island nation, the vessels still have not received porting rights from the Cuban government.
And that wait won’t be ending soon.
Ferries are not a priority, José Ramón Cabañas, Cuba’s ambassador to the United States, told the Tampa Bay Times during a recent visit to St. Petersburg.
For now, he said, Cuba prefers to focus on expanding its cruise industry.
The logistical problem seems to be that ferry operators would want to carry cargo. The Port of Havana can handle passengers but isn’t set up to handle large amounts of cargo; meanwhile, Mariel (the largest cargo port in Cuba, 50 miles from Havana) isn’t set up to handle large numbers of passengers. Without further infrastructure investment, there isn’t a good single destination for Florida-Cuba ferries.
Not yet a real ferry service, but the first US cruise to Cuba is supposed to sail today. http://www.miamiherald.com/news/business/tourism-cruises/article74753237.html
UPDATE: the cruise sailed and arrived in Havana: http://www.miamiherald.com/news/nation-world/world/americas/cuba/article75096132.html
As passengers cheered, Carnival Corp.’s Fathom Adonia arrived at
Havana harbor on Monday morning, officially reestablishing the U.S.
cruise business in Cuba.The voyage of the Adonia, with about 600 passengers aboard, was the
first trip from a U.S. port directly to Cuba in more than 50 years,
and the importance of the historic trip wasn’t lost on anyone.
The first article gives also some details about the legal struggle that preceded the voyage.
My assumption is that the ferry companies are (were?) facing similar problems. But a tour along the websites of some of those companies did not reveal any new information.
This is an update from March 2016. The ferry company mentioned in the other answer now states:
[…] as January 2016, ferry operators are still awaiting final approval and licensing from the Cuban government. Because of this, CubaKat (and other ferry companies) are waiting to begin full operations.
and
CubaKat’s goal is to offer our ferry service, from the Florida Keys to ports within Cuba, some time in 2016. Currently, we’re working with officials from both countries to make this venture a reality.
Whereas at least the second statement sounds more like a marketing statement than a reliable prediction.
The Miami Herald run an article on this last month, and wrote the following
Nierenberg now expects U.S. ferries to be sailing to Havana by late 2016 or early 2017.
quoting and official from another ferry company.
Overall it seems like there is no official answer yet.
Just to provide the answer by @user31253 some flavor since it’s a direct quote:
From official website of one of the Ferry Companies CubaKat
Experience Passenger Ferry Service to Cuba from Florida
In early May 2015, the U.S. government, through the Department of Treasury, began issuing licenses to American ferry operators to provide service to Cuba.
As of late June 2015, however, the Cuban government has not provided licenses to ferry operators. Because of this, CubaKat (and other ferry companies) are waiting to begin full operations.
Credit:stackoverflow.com‘