The article cites distribution as the industry’s worst enemy. Ethanol can’t be pumped through pipelines as easily as gasoline due to its highly corrosive nature, which means the burdon of bringing the fuel to refineries will be placed on this country’s rail, truck and barge infrastructure, any one of which could bottleneck the production process and drive up the fuel’s final cost.
One interesting footnote in all of this is the recent ban of MTBE, an oxygenate that when added to gasoline enables it burn more cleanly. MTBE has been found to pose health risks, so when it becomes phased out completely by May 5th, the refining industry will be looking to ethanol to take its place. Time will tell whether or not the ethanol industry can cope with its product's newfound popularity.