I tend to hit the Cmd-Q instead of Cmd-W when I am closing a tab and in my older installs on OS-X I had changed the shortcut for Safari Quit and that is one thing (among others) that I did not migrate to my new OS-X 10.11 install.

So, open up System Perferences and go to KeyBoards and then the Shortcuts pane and add an App Shortcuts for Safari only for the menu item called Quit Safari, mine now is Ctrl-CMD-Q: