Clearly, the side effects are worth the protection from the lethal bacteria. This is akin to the rabies vaccine, which is administered to people who constantly come in contact with animals, such as veterinarians, but is not administered to the general public. This is prudent medical reasoning, since it is not necessary to protect people who are not at risk of contracting the disease. However, with the real threat of biological warfare, it is important to protect service men and women who could potentially be exposed to anthrax. Antibiotics can stop the bacteria in those infected without subjecting every to the vaccine.
Antibiotics are only effective if they are administered shortly after exposure.
As mentioned earlier, it is nearly impossible to detect anthrax, thus it is very difficult to determine the timing of the exposure and those who may be infected. If a hostile power were to genetically engineer a new strain of anthrax, it might not be neutralized by the protected immune system. Furthermore, it is much more complicated to both engineer and produce the variant anthrax toxin. Since a new vaccine would require years of testing prior to release, the current vaccine gives our armed forces protection immediately. This decision should be left to military and medical experts.