There is a bug in the 2.0.1 WordPress release that causes your main RSS feed to display your comment feed instead of the regular main feed. This seems to only happen if you use a custom permalink structure. The information on the bug can be found here and the official bug is listed here..

The fix (as listed in the above bug report) is to modify /wp-includes/classes.php and change line 1324 (give or take)
from this:

// Comments
$comments_rewrite = $this->generate_rewrite_rules($this->root . $this->comments_base, true, true, true);

to this:

// Comments
$comments_rewrite = $this->generate_rewrite_rules($this->root . $this->comments_base, true, true, true, false);

You then have to flush the rewrite rules by either creating a new static page, or updating your permalink structure. (I choose the latter, which has the unfortunate side effect of marking all of the posts in your feed as new posts, which can annoy subscribers.)