I want to be able to lower all windows and show the desktop from the command line, not
There is a useful command line application called
xdotool which amongst other stuff, allows you to send keystrokes.
Thus - to mimic Control+Alt+D (or Super+D, or whatever the combination is you need), you can use one of the following commands:
xdotool key ctrl+alt+d xdotool key ctrl+super+d xdotool key super+d
sudo apt-get install xdotool