When accessing a page on a site without a FQDN with an RSS/Atom link in it, i.e. http://server/ clicking on the rss link in the address bar causes the brower to be redirected to http://atom/ and generates an error "Safari can't open page http://atom/ ...." If the server name is fully qualified (http://server.intranet/) then the rss page is fine.
This is how the rss feed is linked into the page <link rel="alternate" type="application/atom+xml" title="Atom feed" href="/atom" /> This works without issue in Firefox
This may turn out to be a Safari issue. Since Safari is not open source, those should be reported via <http://bugreport.apple.com> (free registration required). If you do so, please include a link to this Bugzilla report, and then post Apple's problem ID here.
Logged as ID 5333165 on <http://bugreport.apple.com>
I cannot confirm the problem in the latest Webkit r31114 on Mac OS X 10.5. Clicking RSS icon redirects me to feed:http://localhost/~user/rss.xml and the feed is properly rendered.