Today's Washington Post published an article about how surging interest in ethanol as an alternative fuel may increase pollutant flows into the Chesapeake Bay. The crux of the article is that demand for ethanol is causing more farmers in the Chesapeake Bay watershed to plant corn instead of other crops. Corn tends to be more fertilizer intensive, so more fertilizer flows off the fields and eventually ends up in the Bay.
For me, I think the message that keeps reverberating is that there are no silver bullets. Alternative fuels can play a role in helping us toward sustainability, but we have to pursue all paths: more efficient vehicles, better transit services, more well planned communities, etc.