Unfortunately new iOS 6 operating system has a flaw where you need to recreate your bookmark in order for this app to determine your location properly. We highly recommend you upgrade your phone to iOS 6.1 which has fixed this problem.
If you cannot upgrade to iOS 6.1 then first delete the icon you used to open this app. Then open the Safari web browser, go to nextbus.com, and create a new bookmark on your home screen.

Apple has fixed the problem with obtaining your location. We recommend that you upgrade to the new iOS 6.1 operating system to get this fix. Then once you add the NextBus app to your homescreen again it will behave like a regular app and won't ask you for permission to use your location every time!