Basically, sometimes there commands take a long time. It's nice to have feedback that something is happening even if it's just effectively a blinking light.
The only thing worse than a throbber that keeps going until everything is loaded regardless if anything is actively happening is a fake loading screen that lies to you about what it's doing. The only time you should use a throbber without context is when there's only a single action being processed and it's expected to take less than 5~10 seconds.