if you have your mod_rewrite rules correctly in place you should be able to call your pages omitting index.php?/
Since eZ Publish doesn't know anything about it, the generated URL's still contain the index part, that's what the ForceVirtualHost parameter is for, to generate URL's as if you where using the VirtualHost mode.
This is bad... I was wondering where my acp options have gone. It seems that it was not loading the library files, so, after some research, I found on Virtual-host-setup section in the installation manual that we need to change the line