Who is they? The Joint Chiefs? They don't call the shots. They make recommendations. The Commander in Chief can either agree or disagree.
No shit, I think everyone here knows that, but you won't deny that they have other means of applying their case if needed--not even talking coup.
Anyway, this is no where near rumors of a coup. Here's the dirt:
A Pentagon consultant told Hersh more than a year ago, "There is a war about the war going on inside the building." Hersh also reported that Gen. Peter Pace had forced Bush and Cheney to remove the "nuclear option" from the plans for possible conflict with Iran -- in the Pentagon it was known as the April Revolution.
In December, according to Time correspondent Joe Klein, President Bush met with the Joint Chiefs of Staff in a secure room known as The Tank. The President was told that "the U.S. could launch a devastating air attack on Iran's government and military, wiping out the Iranian air force, the command and control structure and some of the more obvious nuclear facilities." But the Joint Chiefs were "unanimously opposed to taking that course of action," both because it might not eliminate Iran's nuclear capacity and because Iran could respond devastatingly in Iraq -- and in the United States.
In an article published by Inter Press Service, historian and national security policy analyst Gareth Porter reported that Adm. William Fallon, Bush's then-nominee to head the Central Command (Centcom), sent the Defense Department a strongly worded message earlier this year opposing the plan to send a third carrier strike group into the Persian Gulf. In another Inter Press analysis, Porter quotes someone who met with Fallon saying an attack on Iran "will not happen on my watch." He added, "You know what choices I have. I'm a professional.... There are several of us trying to put the crazies back in the box."
http://www.cbsnews.com/stories/2007/10/10/opinion/main3352206.shtml