But isn't there something about the anti-oxidant properties of chocolate that also play into it? Or is it really just the protein and sugar values?

Personally, because I tend to believe that the only form of chocolate is in the solid, dark chocolate, I've learned to justify milk chai (iced or hot depending on the weather) instead of chocolate milk after rides. Protein from the milk, sugar from the chai mix and all those good antioxidant properties of tea...and I'm sure that the spices are also good for me somehow.