I think iFly intentionally retains the nav buttons, because the other common option is to have them "hide" off the bottom of the screen, where the user can reveal them by swiping up. But then they'd appear on top of iFly buttons and be hard to see/cause interface confusion (which button are you really trying to press? / Doh! I accidentally swiped up and revealed the nav bar, and now they're blocking my iFly buttons, and I have to wait seveal seconds for them to hide again / etc.).
If your phone supports it, one option is to change to use "gestures" instead of buttons. So instead of tapping the middle nav button for instance, you would swipe up from the bottom middle of the display to get that function. That's a global settings change, though--AFAIK there's no way to set it to use gestures only when iFly is running. Your phone may differ, but on mine, I go to Settings > Display > Navigation Bar. On this page, I pick "Swipe gestures" instead of "Buttons". I can also choose here to show "Gesture hints" or not--if selected, three horizontal lines will still be reserved at the bottom of the screen to remind you where to swipe, but if unselected the app will fill the whole screen to the bottom bezel.
Since this is more of a "how does my phone work" question rather than a "how does iFly work" question, if my info above doesn't help, then you may get better results just Googling, or maybe asking on a forum that supports your phone specifically.