The navigation bar only disappears automatically after you selected a book in your library. It is displayed for a few seconds to show that there are controls. After it disappeared you can make it appear by taping anywhere. It works analogous to the video player.

So it’s consistent with other navigation controls that don’t have to and probably shouldn’t be displayed all the time.

Once you tap the text to make the navigation bar show up it won’t disappear automatically – ever – at least as long as you are reading the same book and don’t go back to your library, no matter where you switch to.

One of the problems with the current behavior is that anywhere doesn’t really mean anywhere inside iBooks. The left and right margins are reserved for turning the page. That can frustrate users who want to make the controls appear. If they tap the wrong place they turn the page instead of making the controls appear. There is no obvious demarcation about safe places to tap. Making the controls disappear when playing a video works better because users really can tap anywhere. There are no unsafe spots.

Here is how I would change it: I would just not hide it by default. Users would still be able to hide it by taping on the text.