I think what the articles reference is correct. The clearing of forest ect. will have a negative effect on the climate. Also, the fertilizer needed for crops such as corn has negative effects on the eco system. Sometimes very far from the source. I don't think the article is fair to all forms of biofuels though. I see biodiesel and alcohol (E85) produced from wate products as a win-win situation. There is a cost for disposal of waste. I think alge based biodiesel or biofuels will be the way to go. From what I read its still about 3-5 years away from being comercially viable. My understanding is there is some waste from biodiesel production (glycerin). This can be converted into alcohol. So more fuel.
Tom