@mailer You have got the syntax slightly wrong, and need to escape special characters.
This works for me to exclude <code> elements and php code
$settings[] = "protectedSource: [/<code>[\s\S]*?<\/code>/gi,/<\?php>[\s\S]*?\?>/gi]";
<p><code>this cannot be edited</code><?php> neither can this ?>but this can be edited</p>