As of 2003, Dunn & Bradstreet ranks Cuba in the top 5 of greatest risks in the world, alongside Iraq, Zimbabwe & Angola. They have over $1-billion in defaulted debt at that time, probably more now.
No for-profit enterprise would do business with anyone with that type of credit risk unless paid in advance, in hard cash. And even if Cubans came to a Hilton Hotel with cash, I'm sure Hilton would expect to apply it as payment for existing debt before any new transactions.
According to the regional spokesperson for Hilton, the refusal was due to the risk of legal sanctions against Hilton in the US for breaching the boycott.