The U.S. military's "going green" is not a singular phenomenon. There are several different things going on under that rubric, with different rationales and different effects. Some of them make such obvious strategic, economic, and environmental sense that no one really can, or does, oppose them. But one in particular -- the biofuels initiative -- is much less clear-cut. Before discussing that, though, let's try to pick apart and categorize the green initiatives underway at the Department of Defense.
First off, there are attempts to reduce fossil-fuel use in the theater of war, mainly Iraq and Afghanistan, through more efficiency (insulated tents, LED lights) and the use of distributed renewables. These efforts directly enhance battlefield effectiveness. They make fighting units lighter and faster. They reduce the need for fuel convoys, saving lives and money. They are unimpeachable -- even Republicans in Congress will hesitate to second-guess the military's tactical logistics decisions.
Second, there are attempts to make U.S. military bases more independent of civilian power grids, which are vulnerable to accidents, blackouts, or attacks. In part this is being done by generating power on-site. Solar power for bases has become far more affordable, thanks to plummeting solar-panel prices, but there are also experiments underway with wind, geothermal, and biomass. Bases are also increasing energy and waste efficiency and experimenting with smart microgrids. These efforts seem somewhat more vulnerable to political attack, but I've not yet heard of any.
Third, there are efforts to find new liquid fuels for the military's vast land, air, and water fleets. This one is the biggie, from the standpoint of sheer quantities of energy and money. It's the most difficult. And it's also the most controversial, in terms of Republican opposition and environmental risk.