That's an interesting point. Since the "Rules" entry is in the "Article" menu, I wouldn't have thought to look in the right-click on Subs. Consistency issue? Are rules sub or article focused?
I'd still like an "Apply Rules" straight after the "Rules" (which should probably be "Rules..." because it opens a panel) menu entry, whether that's in Articles or gets moved to Subscriptions for consistency. Or maybe a new Tools menu at this rate, alongside ROT13 and Local Search and the forthcoming Global Search you mentioned in the search thread.