Ethanol is a joke, still energy net negative when you consider the cost to grow and process from Corn. Bio Diesel on the other hand, is energy net positive growing the proper crops.
The problem is that Ethanol is subsidized so it is being made artificially more attractive. It is asinine public policy to promote the use of anything by artificially subsidizing it. Energy creation is expensive and difficult and the methods used should be the ones that are the most cost effective.
Oil is currently the most cost effective, but at some price, it won't be. That's when you'll see the alternative methods appear. And the answer is not fuel cells.