I see the following in the codex (Create A Network), and I'm wondering if this has now been addressed. I just installed a brand new WP3.3 RC2 multisite install, and my permalink structure still has the /blog/ in the URL.
Sorry if this has already been answered somewhere, but the most recent I see on this subject is from 7 months ago.
Thanks!
While permalinks will continue to work, the main site (i.e. the first one created) will have an extra entry of blog, making your URLs appear like domain.com/blog/YYYY/MM/POSTNAME.
This is by design, in order to prevent collisions with SubFolder installs. Currently there is no easy way to change it, as doing so prevents WordPress from auto-detecting collisions between your main site and any subsites. This will be addressed, and customizable, in a future version of WordPress.