This study, widely quoted here, completely ignores the value of any other product that results from the process.
For instance, if "corn requires 29 percent more fossil energy than the fuel produced; " suppose they're right and it takes $1.29 of corn to generate $1 worth of fuel. However, we also get, say, $0.50 worth of animal feed and $0.10 worth of carbon dioxide. In that case, we haven't lost $0.29 on the deal, we've gained $0.31.
The $ figures are purely hypothetical but the point is that these guys only counted the value of the fuel output from the ethanol generation process and nothing else.
Excellent, then we don't need a subsidy.
It also does not take into account government subsidies and tax credits that add unknown additional costs to the consumer/taxpayer. This would negate any cost savings via biproduct sales.