the most unnerving legacy of the Bush administration is the encroachment of the Department of Defense into a striking number of aspects of civilian government. Our Constitution is at risk.He argues that we need to
reverse the current trend of Pentagon encroachment upon civilian government functions, or they could complete the silent military coup d'etat
Despite this ridiculously hyperbolic language, the rest of the article is actually worth reading. Although some of his fears border on paranoia, he makes a solid case that the Pentagon has too much power vis a vis the State Department, the Justice Department, and other agencies involved with U.S. foreign policy, and notes that former & serving military officers have been dominating civilian agencies. He gives specific proposals to reverse this trend, including getting rid of Rumsfeld holdovers, putting more civilians in charge of important positions, and transferring money and responsibility away from the Pentagon in some areas.
UPDATE There's a good critique of the article here