Congress has the power to declare a war, which was supposed to prevent the Executive from taking any military action that was not purely defensive, without their approval. There was even a requirement about how long the President had to give an accounting to Congress about any action they did take. So yes, Congress was supposed to have the ability to "command" the military insomuch as they could choose whether the Executive could utilize them or not. Saying "no, you're not going to do that" is an authoritative command.
Hamilton, Washington, and Madison all separately wrote that Section 8's War Declaration clause was intended to be a substantial limit on the President's power. Even the small, mini-conflicts in the 1800s required Congressional approval to initiate, it wasn't until the 1950s that the Executive branch destroyed that check on Executive power.
By command I meant that Congress cannot tell the military "go arrest the president" or "go quell the unrest in that state." I agree that Congress has ceded too much power to the Executive in regard to declaration of war/military action in foreign countries after 9/11 though.
Trump may be Commander in Chief, but he cannot start a war without Congress' approval.
Unfortunately, they've essentially given more or less blanket approval for various wars and war-like actions since before 9/11, and that approval keeps getting renewed every year.
