Related link: http://www.xml.com/pub/a/2004/06/16/dive.html
RSS and Atom are all about providing metadata to help someone or something decide whether to follow a particular link. The Atom effort is making an admirable effort to include link typing with a taxonomy based on HTML a/@rel values. This re-use, like much software re-use, has led to the use of something, just because it was available and part of the set being re-used, that doesn’t fit well where it’s being applied (the use of the term “alternate” to indicate a primary resource) but sensible people seem to have noticed this. Other HTML a/@rel values work as well in Atom as they were supposed to in (X)HTML.
Mark Pilgrim’s XML.com article explains the use of Atom’s link/@rel attribute, and I’ve added a comment underneath the article. I must admit, I haven’t followed the Atom work very closely, so I’d be happy to hear any clarifications about this.