Amongst what was mentioned in the article, Toyota's North American sales have been benefiting from Japan's currency manipulation for years. Considering Japan's unwillingness to stop tilting the playing field, I don't see anything wrong with the American government doing something to encourage American buyers to buy an American product.
Besides...if they want to do something about it, they can engineer a Prius with a 6-kilowatt storage capacity. Their customers can reap the tax break, they can reap the sales, and it'll all be gravy.