I see there is a new documentation page for virtualhost configuration in ez publish 5.x.
http://doc.ez.no/eZ-Publish/Technical-manual/5.x/Installation/Virtual-host-setup

I think it won't hurt to add <IfModule mod_rewrite.c>

RewriteEngine On

in the <IfModule mod_rewrite.c> part.

I needed to do it to have rewrite rules working.