Actually, my worst was a couple of years ago when I got on a Tropic flight at the Municipal for San Pedro. We made three stops - International, Caye Chapel, Caye Caulker. The flight took almost 50 minutes!
Mind you, it was the best view of Caye Chapel I've ever had. Shame I didn't have a camera with me.
Elbert's right - get the extra cost into perspective. The hassle of driving to the Municipal just isn't worth it.