I had the same problem, but the RewriteRule solution proposed by gloddy didn’t work for me, so I decided to simply redirect the whole thing:
Redirect /wp-rss2.php https://www.yoursite.com/feed/rss2/
Redirect /wp-rss.php https://www.yoursite.com/feed/rss/
Redirect /wp-atom.php https://www.yoursite.com/feed/atom/
I hope this helps. I’m not quite sure wether some RSS readers have a problem with being redirected, but it seems to work fine with Bloglines and Thunderbird.
