I have been to Cuba many times in my role as a member of the media (one of the exceptions granted for travel to Cuba is for the media under the doctrine of freedom of the press contained in the First Amendment)
The travel restriction to Cuba applies to spending money in Cuba so I would agree with other posters that if CO were to sell a ticket that involved travel in (or through) Cuba, Continental could likely get in trouble, because, even though no Cuban carrier is involved, part of the ticket cost covers Cuban airport fees and taxes.
As far as whether the traveler on this itinerary could get in trouble, I am not a lawyer, but I would imagine the same principle would apply, namely that the traveler would have spent a portion of the ticket purchase on Cuban airport fees and taxes and thus violated U.S. law prohibiting spending in Cuba.
I would imagine that the actual trip to Cuba would not be an issue, simply the revenue transferred to the Cuban authorities through the ticket purchase.
Cuba is not only interesting because it is a stunning timewarp, but it also happens to be a gorgeous Caribbean island with very friendly people and wonderful beaches.
Cuba today is overrun with tourists from virtually the entire developed world, including legions of Canadians and Europeans. But there are precious few Americans, except for the occasional journalist, filmmaker, and those who take those organized tours usually through Mexico.
Those with relatives, of course, continue to be allowed to visit on humanitarian grounds. The irony is the Miami's Cuban community, which is vociferously anti-Castro, remains one of the more significant sources of hard-currency income for the island.
Someday the Castro brothers will no longer control Cuba and there will be some major changes.