Usually, a vaccine isn't allowed to be used by the general public until the FDA has ruled that there is evidence that it is both safe and that it works. Such evidence usually comes from using the vaccine on people who are likely to be exposed to the disease in question. But that doesn't mean that the vaccine would work against anthrax used as a weapon. Making decisions means something different in the military, and soldiers don't get to exercise choice in many aspects of their lives. Part of serving in the military is to accept the risks of training and service, whether it be plane crashes, combat hazards, or the side effects of vaccines.
Soldiers have different rights and obligations than civilians.
Soldiers must follow the rules dictated by their branch of the service, and in return the military is obligated to assure that the troops are ready to serve. Second-guessing by soldiers about what counts as readiness would lead to dire consequences. Since 1998, the Department of Defense has been vaccinating all active and reserve soldiers against anthrax. But more and more soldiers are refusing the vaccine because of uncertainties about its safety. Last week a Congressional panel recommended that the inoculation program be stopped until tests show the safety and efficacy of the vaccine, but the Pentagon has refused to stop the program.