Users don't view file browser windows as belonging to an application as much as they view them as belonging to the computer itself. Using Ctrl+Q as you suggest is misleading because (1) Ctrl+W is used to close windows, is this is likely what the user intended to do (rather than quitting Nautilus) and (2) quitting semantics in this case would close all Nautilus windows, which certainly seems counterintuitive.
Users don't view file browser windows as belonging to an application as much as they view them as belonging to the computer itself. Using Ctrl+Q as you suggest is misleading because (1) Ctrl+W is used to close windows, is this is likely what the user intended to do (rather than quitting Nautilus) and (2) quitting semantics in this case would close all Nautilus windows, which certainly seems counterintuitive.