Things don't always appear to be exactly what they are. Slowly this seems to be the growing realisation with biofuels (as described in this article)

Earlier this year, two important scientific studies were published that pulled the rug out from under the biofuels movement, and market. First, a Swiss government study (Zah, et al.) determined that biofuels were worse than fossil fuels in terms of total environmental impact, because cultivation of biofuels was driving the destruction of natural ecosystems for agriculture. Even my Brazilian sugarcane ethanol, according to this assessment, was directly to blame for destroying natural systems. Rising demand for ethanol generally was also causing major indirect, but even worse, destruction. For example, US farmers have been switching from soy to corn, for which they get special biofuel subsidies as well as increasingly high prices. Then Brazilian farmers cut down rainforest to meet the increased demand for Brazilian soy. I stared at the graphs for a long time, but there it was, in hard-to-deny numbers: overall, my ethanol car was hurting the environment, much more than I had previously known, and more than my neighbors' "normal" cars, on which I had been looking with such negative judgment.
It is a nice human perspective which covers the different angles without delving into the scientific detail (which can all be found by googling).