This question is probably better suited for one of the other forums. (There's one on Cuba specifically: FlyerTalk Forums > Travel&Dining > Travel&Dining: Destination >> The World >>> Cuba.)
Anyway, I just returned from Cuba. I flew the "official way" via MIA. All the US flights are charters controlled by the US Dept of Treasury.
As a non-American, you can fly there via
-Mexico (although I heard the flight/plane is a bit scary/rickety)
-Bahamas
-Canada
I'd suggest that you do one of those routes to avoid the extra paperwork.
If you have questions about the best routing, I'd suggest emailing the folks at Marazul
www.marazul.com . . . they are a travel services company specializing in Cuba travel. I've found them to be pretty responsive over email. And, they were LIFESAVERS in helping me get there last week for a conference AND in helping me return early when I learned that a family member fell ill.