CM Airlines, a small regional carrier that flies between Roatan, Utila and San Pedro Sula, also offers occasional charter flights to Copan. You can contact them from their website. I believe the Copan "airport" is right on the border with Guatemala, maybe just across the border,... probably 5-8 miles away from Copan Ruinas. I've never flown in there so I don't know if it's a grass strip or not. If it's a small group of people you could probably arrange something with CM directly or work through a local Copan contact such as MC Tours or maybe Twisted Tanyas.
Frankly, though, if you have time I'd get on the Hedman-Alas bus from San Pedro to Copan; it's nonstop, comfortable and relatively inexpensive.