iOS 6 may have separate podcast and iTunes U app
Of course, just because podcasts won't be in iTunes doesn't mean that Apple is banishing them all together. Instead, sources say that iOS 6 will have a new app that is separate and just for podcasts. If that's true, that means that podcasts will get its own app (as iBooks did, and video), which would take podcasts out of iTunes and also of course out of the Music app. It seems like this is happening because the next version of iTunes that Apple showed developers doesn't have podcasts, although there is no separate app as yet in iOS 6 beta.
Additionally, there is a rumor that iTunes U will also be getting bumped out of iTunes and into its own app, but there has been no confirmation on that.