Windows uninstaller removes all directory, including user files
The title says it all. These three line seem to be the culprits:
RMDir "$SMPROGRAMS\VideoLAN"
RMDir /r $SMPROGRAMS\VideoLAN
RMDir /r $INSTDIR
It should instead delete only the files installed by VLC and delete the directories if no user files are left. (or ask if the user wants to delete them)