WordPress permalinks confusion

It is the way the .htaccess wordpress generatea instructs apache to work on the wordpress directories

The relevant parts from the default .htaccess

RewriteCond %{REQUEST_FILENAME} !-f
RewriteCond %{REQUEST_FILENAME} !-d
RewriteRule . /index.php [L]

The first line will cause the rewrite engine to bail out if there is a file with the same name as the server is asked to serve

The second line will cause the rewrite engine to bail out if there is a directory with the same name as the server is asked to serve

The third line is what actually invokes wordpress and you will not get to it if you bailed out on one of the first two lines.