Apache has a nifty mass vhost feature. Problem is, when I use this to reach my site, clean-urls stop working. Is there a way to combine this with clean urls?

<Directory /var/www/localhost/htdocs>
  Order allow,deny
  Allow from all
  AllowOverride
</Directory>
UseCanonicalName Off
LogFormat "%V %h %l %u %t \"%r\" %s %b" vcommon
CustomLog /tmp/access_log vcommon
VirtualDocumentRoot /var/www/localhost/htdocs/%0/web
VirtualScriptAlias /var/www/localhost/htdocs/%0/web

Obviously I've attempted to add

RewriteEngine on
RewriteBase /
RewriteCond %{REQUEST_FILENAME} !-f
RewriteCond %{REQUEST_FILENAME} !-d
RewriteRule ^(.*)$ index.php?q=$1 [L,QSA]

to the <Directory/>, but that doesn't help.