This checkbox lets you control what Sloop does when the cursor is over the background desktop. If ignore desktop is on, Sloop won't do anything when the cursor is over the desktop. If ignore desktop is off, Sloop will switch to the Finder when the cursor is over the desktop.
However, Sloop will never switch to the Finder if you have added the Finder to the Don't switch to these list within the Application preferences dialog box. That list overrides the ignore desktop setting.