DirectoryIndex controllers/index.php
RewriteEngine On

RewriteCond %{REQUEST_FILENAME} -f [OR]
RewriteCond %{REQUEST_FILENAME} -d
RewriteRule ^ - [L]

RewriteRule ^$ controllers/index.php [L,QSA]
RewriteRule ^([A-Za-z0-9_-]+)\.php$ controllers/$1.php [L,QSA]