Basically pollution, resource destruction, and expense; from the OP:
> But today, the downsides of that kind of farming are becoming all too painful. Excess nitrogen fertilizer runs down watersheds to create vast dead zones in the Gulf of Mexico and elsewhere around the world. The rich soils of the U.S. Midwest or Ukraine, grown over thousands of years by billions of grazing animals, are almost gone, damaged by relentless plowing, blown away by the wind or washed away by storms.
> Everywhere, farmland is becoming increasingly acidic, demanding additional liming. Vast monoculture plantations act like an open bar to pests and diseases, forcing farmers to spend more and more on pesticides. Aquifers are being sucked dry, raising the cost of irrigation as new wells must be dug ever deeper. Industrial farming is engaged in a vicious circle of ever more inputs at ever greater expense to try to keep up with the challenges it creates.
> And often, it fails. About a third of the planet’s farmland has already been abandoned because of soil degradation.