Senator requests better https compliance at US Department of Defense [pdf]
AFAIK, the point of the DoD Root CA is to avoid trusting an external entity not to intercept military traffic. Most .mil HTTPS sites that are intended to be accessed by the public (like <a href="https://www.army.mil/" rel="nofollow">https://www.army.mil/</a>) are signed by a regular Root CA, while internal sites use the DoD Root CA.