You, most assuredly, are misinformed.
UC scientist says ethanol uses more energy than it makes:
http://www.sfgate.com/news/article/UC-scientist-says-ethanol-uses-more-energy-than-2659237.php
Study: Ethanol Production Consumes Six Units Of Energy To Produce Just One:
http://www.sciencedaily.com/releases/2005/03/050329132436.htm
Efficiency and Environmental Improvements of Corn Ethanol Production (The Net Energy Balance focuses on whether it takes more energy to produce ethanol than is contained in the ethanol. The answer to this question is yes. If it took less, ethanol production would be breaking the laws of physics and creating energy where there was none before.):
That is only true if you count the “solar power” used to grow the corn.
The Energy Balance of
Corn Ethanol: An Update
http://www.transportation.anl.gov/pdfs/AF/265.pdf
Here is the actual study your links reference by Tad Patzek.
His energy inputs include the food the farmer eats and the solar power used to grow the corn. His calculation include the inefficency of the the corn use of solar energy versus solar panels.
http://gaia.pge.utexas.edu/papers/CRPS416-Patzek-Web.pdf
This study is BS and refuted by many differenct sources.
To be clear, that is using the solar power used to grow the corn. If you are going use that standard, every form of energy we use containes less power than the power used to form it.
Oil & Gas is ultimately formed from solar power growing of the algea, plankton and the like that was depositied in sea and lake sediment and used heat and pressure from the earth to breakdown into the hydrocarbon molecules we harvest via drilling. If you want to include that junk, it may make for technical paper, but has no meaning in the real world.
Likewise, you, as well as most people, are misinformed.
The ideologists have successfully framed this issue/argument around the relative efficiency/cost versus gasoline and the relative emissions versus gasoline.
The use of ethanol as fuel was because of the trade deficit.
A very large portion of our trade deficit is attributable to imported oil and at that time we were importing 70% of our oil and the price of oil was escalating, substantially raising our deficit. When oil went to $60 it doubled that portion of the deficit and at $90 it tripled.
This was exactly the same reason Brazil went the ethanol route decades ago.
The second part of mis-information you are falling for revolves around corn.
The ultimate goal was to produce cellulosic alcohol. The fermenters/distillers were allowed to kick off using corn because they could get quick cash flow and use the profits to pay the R&D cost to develop the enzymes to ferment the cellulose. That would become a problem because it took longer than expected.
Written into the legislation and the regs was the requirement that gasoline producers begin using cellulosic alcohol on a certain date in the future and if they didn't, they would be subject to fines. But because the technology development lagged, they were paying fines for not buying something that wasn't available. So they were given relief.
The third part of the mis-information you are falling for is the value of the corn and how it may affect our food supply. We export huge amounts of corn at a very low price(NAFTA). Any amount corn diverted from export market to alcohol market undergoes a value added process and adds to jobs, corporate profit, and GDP.