I had the same problem with a single site configuration (where the settings.php is in sites/default and not in sites/example.com). I was wondering because with the --dry-run option I didn't get any error.
I guess, that the folder containing settings.php will be set to read only by the drupal installation script.
So you may run chmod u+w sites/default/ in drupal root before patching drupal and chmod u-w sites/default/ after patching.
chmod u+w sites/default/
chmod u-w sites/default/
Weitere Informationen über Formatierungsoptionen