US citizens are not permitted to travel to Cuba without special permission from the Department of Treasury. This also includes "payment for air travel to Cuba".
Source: U.S. Department of Treasury, Office of Foreign Assets Control, Part 515 Cuban Assets Control
Whether you get caught or not is another matter (they won't stamp your passport), but personally I wouldn't risk it just to save a few bucks on airfare. A long-haul flight on Cubana doesn't sound that comfortable to me and if you end up getting stuck in Havana due to delayed flights, etc. things could get complicated if you want to avoid entering the country.
You also need to be careful how you pay for tickets. If you pay with a US-based credit card for example, and they find out (or suspect) the payment is for a travel to Cuba, the transaction will be blocked and you will probably lose the money and perhaps find yourself in other trouble. Even if your credit card is from a foreign bank, you might find that the transactions get cleared or pass through the USA anyway, putting you at risk to having them blocked.