Non WordPress Folder in a WordPress Site

You can revert to the default WordPress rewrite rules. This line already handles checking for existing physical directories:

RewriteCond %{REQUEST_FILENAME} !-d

Your problem does not lie with WordPress, but with some other problem with your server/htaccess files. You have not provided enough information to solve your problem, but it probably is an issue with file permissions, Deny from rules in htaccess, or indexes.