Then again Miami International Airport will most likely have dozens of flights per day to Cuba once things get going, perhaps even several by the likes of Southwest and Jet Blue. So perhaps Amtrak should remain at Miami Airport Station afterall.
It is also likely that the likes of Orlando will get several flights a day to Cuba too, and Orlando International will eventually get connected to Orlando Amtrak by SunRail.
If Cuba-US air travel is truly opened up, you're going to see multiple daily non-stops from Cuba-New York. (In fact, those flights already exist on a charter basis). There are currently Cuba nonstops from Tampa, Fort Lauderdale, Chicago and Los Angeles, as well. (and likely more) Orlando flights are
starting this summer.
The point being, if someone in Cuba can afford a plane ticket to Miami or Orlando, they'll also be able to afford a plane ticket to NYC or any other east coast destination (via connections). The airfare Cuba-MIA will not be appreciably different from the airfare Cuba-NYC or Cuba-WAS, etc due to the way the airline pricing works.
In short, IMO, the improved relations with Cuba will not have an appreciable impact on Amtrak's east coast operations. Market to Cubans? Sure, why not. But the number
of Cubans who would fly into MIA and then take a Silver Service train to, say, Yemassee or Sebring is negligible.