Get cursor on top, where white header with file name, then press Alt.
To set top menu by default always visible.
You needed in top menu selected:
FILE -> Config... -> autoHideMenuBar: true (change it to autoHideMenuBar: false)
Save it.
I had the same issue and Alt did not work for me. If you go into the config (mine was in users/{user_name}/.atom/config.cson), you will see a line for hidden tool bar, remove that line and restart Atom.
There is probably a value you can set it to besides "hidden" but I did not figure it out