lunabyte,
First off, this in no way to be taken as ungrateful or disrespectful to those giving away WPMU. However, I have spent hours digging through this forum, specifically for this topic.
With all of the posts on this topic, maybe the ones overlooking this issue aren't the users? Yeah, I can set up redirects to help cut out the original sub-directory, but that means I have another piece to manage.
If I just leave the sub-directory in there, it's more characters to type, put on promo material, etc. The professional looking URL for my sites does not allow for WPMU to be the primary install, or to have a /blogs/ or /users/ or whatever in the URL.
The problem does not seem to be a technical issue. The problem seems to lie in a lack of programing. There is code to do this. (Here is a post to follow: http://mu.wordpress.org/forums/topic.php?id=6802.) It doesn't make sense to require that WPMU be the primary index.php file of the root directory for this to occur.
Sincerely,
gah242s
P.S. I registered simply to write specifically to you. Your language is consistently degrading.