If you use WordPress on your root web folder, subdirectories password protected with .htaccess do not work. Users will not get the ability to put in their username and password to access the page. The Apache rewrite rules included in WordPress will forward users to the 404 error page instead.
To get around this, you will need to create a 401 error page in the web root directory (e.g. ~/public_html/401.html) and add the following line to the .htaccess file located in your web root directory.
ErrorDocument 401 /401.html
This also works for other apps using Apache Rewrite Rules, such as Drupal.