Safari Reader does not appear on pages with multiple links - the RSS button appears instead (as on these forums).
If you go to this CNET article about Reader"
you will see the button to the left of the reload icon. However I see no way of annotating the result, it's intended simply to display the main content free of clutter.
If you want to annotate a page you can bring up the Print dialog, select PDF, and then Save as PDF. You can open that in Preview and annotate and save the article.