I have to mostly agree with Mr. Cowford. Anticipating a significant amount of Northeast US-Cuba rail-sail traffic is absurd. 99%+ of the market is going to be owned by 737s and A320s, either direct or connecting through KMIA and KATL. However, I think the rail-sail journey to Havana will eventually be possible to cobble together, but only out of components that will be primarily for the benefit of entirely different markets.
The key will be (in a familiar refrain for American railroading) the demands of freight traffic across the Florida Straits. The overall volume will be highly dependent on political decisions, both bilateral and internally to Cuba, but it seems highly probable that there will be some, and the question becomes how it will be served. Even the most successful ferry routes in Europe, whether they run across the Channel, the Irish Sea, the North Sea, the Baltic Sea, or any of the arms of the Mediterranean, are primarily oriented around truck traffic. Walk-up passenger service, while a nicely profitable sideline, does not pay for the boat. On the other hand, once you have to build a Ro/Ro ferry for trucks, there's no reason not to build a slightly bigger boat for passenger car drivers and walk-up passengers, because doing otherwise is throwing money away. (If you've ever wondered why Eurotunnel trains have never captured much more than half of the cross-Channel market, this park of the economics of ferries is why.)
The question becomes, will there be enough time-sensitive goods trading back and forth to warrant RoPax ferry service, or will US/Cuba trade be happening solely by containers, stacked high on on slow container ships? Unlike Ro/Ro ferries, there's no significant economic incentive to add passenger facilities to a container ship. Part of the answer will have to come in the form of another question: will Cuba's ongoing investments into its own internal transportation be primarily oriented towards its roadway network, or its railroads? If Ferrocarriles de Cuba can improve the reliability of its own service, that might tip the balance in favor of all-container intermodal. If the improvements go to the autopistas, then you will see more truck and car traffic drawn across the Straits.
To bring this back to Amtrak, the more I consider this, the more I think that the primary impact to Amtrak will be to the Auto Train, not to the Silver Service. Although the overwhelming majority of Auto Train traffic will always be for Central Florida, and most of the balance for South Florida, I can definitely anticipate a period where many Americans going to Cuba who want to have a car, will have to (or prefer to) bring their own. The Auto Train is still the time-effective and (usually) cost-effective way to do that from the Mid-Atlantic and New England. I'm on-record (in the Auto Train threads) as thinking the way forward for that service involves more capacity derived from the present terminals, which will necessarily involve a second daily round-trip. Any increase in demand, in my view, will only accentuate that case.