If you want to run eZ publish without "index.php" appearing in the URL, I think you need to have the rewrite rules in apache conf, not in a .htaccess file
I have seen one or two postings from people who reckon they have made the .htaccess rewrite rules work. Guess I'll just have to stick with the Apache vhosts.conf option. Not so easy on a shared server, but the guys who host my sites are pretty helpful.
If your hoster runs Confixx 2 and above, and offers frontpage extensions, ask them to enable them on any (new and unused) subdomain pointing to your root (like 'frontpage.yourdomain.com' pointing to '/'). Without doing so, the rewrite engine does not work if you put it into .htaccess.