If you take arable land away from producing any other food it affects price and supply, or it depletes the soil that may have future purpose. Perhaps that's OK IF the need is there and not a boondoggle. Biofuels are a boondoggle and would have gone nowhere without provisions demanding their use to dilute gasoline and without subsidies. Just another pork barrel project.
We pay in our taxes, we pay at the pump, we pay in reduced mileage/performance/reliability regardless of whether we pay at the grocery.