Beat me to it... I was on one of the (regularly scheduled) Sky King charters to Cuba this January and they applauded both times.
On the flight there, it made sense since we were scheduled for a 1pm departure, and didnt get to Havana until 11pm after the company was on their last plane due to problems with the other two, and we had taken off once already and turned back due to a problem with the engine bleed air.
I actually enjoyed the applauding, but I can see where it gets old if you travel regularly.