I'm sorry you have no understanding of the structure of the government of the United States. But, in fact the Secretary of Defense does command the troops and officers of the United States military and does so with the unilateral authority of the President of the United States, the Commander-in-Chief.
The position of Cabinet Secretary in any department is not that of a figurehead or a policy and budget person but as an executive, a manager, a director; and the United States military answers exclusively to the civilian chain of command.
Be less ignorant be more American or shut up