As a developer it is hard to make everyone happy. I got a lot of requests to make the on-screen buttons automatically hide when flying, so I decided to implement that. I figured it wouldn't do much harm even to those who are using them, since they re-appear as soon as you move the mouse a little.
And even if the buttons are hidden you can still access the options by pressing the shortcuts on the keyboard.
(You can sort of get the buttons to be visible at all times when flying by pressing "v" after they have become hidden. They will automatically hide again when the scene is reloaded (after a crash for example), or when you move the mouse, so it's admittedly not very practical).