I know this is an old question but I've been doing something similar just by adding something along the lines of
RewriteBase /flight/
in the .htaccess file (before all of your rules) of the flight directory. Hope this helps someone else looking for the same thing. Example:
RewriteEngine On
RewriteBase /flight/
RewriteCond %{REQUEST_FILENAME} !-f
RewriteCond %{REQUEST_FILENAME} !-d
RewriteRule ^(.*)$ index.php [QSA,L]