What was going on in Cuba that made the United States uncomfortable with Cuba?

In short, radical socialism/communism. Americans were able to exploit cheap labor and perfect farmland from Cuba, which had a government willing to cooperate with the US. When Che Guevara and Fidel Castro won the revolution and instilled communism, America lost a major source of cheap importation. Also, the communists were vocally anti-American, which was viewed as a clear threat. President Kennedy attempted to topple the Cuban government with the Bay of the Pigs invasion, however, that was a quick failure. Within 24 hours, what was left of the American landing force surrendered and withdrew. The loss of life was not taken lightly by Americans. Trade embargoes were placed when the Cuban dictatorship would not cooperate, leading to the two nations become desperate for retribution. The USSR, in classic Soviet fashion, saw a chance to fight the west through a newly-communist nation. They armed the Cubans and placed missiles on the island, aiming them directly at major cities. The US wasn’t exactly happy about this, so the chaos of the Cuban Missile Crisis ensued.

The dethroned emperor!