The whole idea of an app like Instapaper (or any of the other examples presented) is that the "stuff" that is saved for later is all user-generated content. Some articles may even vanish (different location, move behind a paywall, deleted, etc...). In this case those articles would become inaccessible when the OS deletes the cache.

It seems that the argument that only the list of metadata is user-generated can apply to any type of media (music, movies, etc...). Technically speaking all of the music on my phone could be downloaded on demand. Of course this requires an always connected, fat, and cheap network connection. Which is pretty much the opposite of what most folks have.

This also breaks the user's expectations. I was annoyed/surprised when I upgraded to iOS 5 and Instapaper had to re-download everything.