Why would an aztec receive five rabbits in exchange for fifty cocoa beans?

The reason is very simple - profit.

The rabbits were not worth much to the Europeans, but were to the Aztecs, but the cocoa beans for the Europeans were like gold. They were a very attractive exotic product from which unique and unseen things were made. In the European market the cocoa beans had enormous price, and the demand for it was very high especially from the aristocracy which loved it and didn't speared money for it.