This comparison, often made by Max Boot, doesn't hold up. The Phillipine insurgency was different in an important way from the Iraq insurgency. Most notably, the Phillipine insurgents hardly had any guns and were generally armed with knives and machetes. They had disarmed themselves shortly before the U.S. occupation began. Iraq, by contrast, is awash in guns. Despite the lack of guns by the insurgents in the Phillipines, over 2,000 American troops died.
As with all historical parallels, there is no direct link to be made; one has to go with the best available. In terms of domestic U.S. politics, the local insurgency (not the methods, but its type and motives), the war that led to it, and the U.S. goals for the occupied land, the Phillippines occupation offers the best relation to what's going on now, far better than what happened post-WWII in Germany or Japan.
Furthermore, there were about 200,000 killed in putting down the Philippine insurrection. With today's international media where everything is either instantaneous or recent, there's no way public opinion would accept something like that. Max Boot's an idiot.