She has a reputation that 'commands' attention/respect. [=people give her respect/attention because of her reputation]
In the United States, the President as the commander in chief is at the head of the military 'chain of command'.
She seems to be 'in (full) command of' the situation. [=she seems to have complete control of the situation]
(..) to the greater worlds the Tesseract will unveil. You don't have the Tesseract yet. I don't threaten. But until I open the doors, until your force is mine to command, you are but words. You will have your war, Asgardian. If you fail, if the Tesseract is kept from us, (..)2012 The Avengers