There are several reasons why we our relationship with Cuba is rather sour. I'll set up a list.
1) Their role in the Cold War; remember the Cuban missle crisis? It kind of sent any good impression of them to hell.
2) Fidel Castro. The man is just not fit to rule. Between the execution of his political opponents, his ban on religion, his role in the Mariel Boatlift, and his policy on torture... he's just bloodthirsty man. It's what you would expect from a guerilla fighter and revolutionary.
3) Communism. The problem with Communism is that it basically gives the government complete control of the economy... thus making the people slaves to what the government says. Whatever the government says your dollar is worth, that's what it's worth... it's not backed by trust. It makes it impossible for you to live beyond your country of origin, as your currency is only worth paper/metal/whatever anywhere else.
Cuba itself isn't a bad country; they're actually quite civilized and advanced for a Latin-American country. The main problem is Mr. Castro, and his continued infringement on basic human rights.
But as far our relationship with Cuba... I'm willing to say it's gotten much better in the past decade. I mean, moving from open hostility to a sort of uneasiness is quite an improvement, compared to where we were.