So you are saying that the lean up/down keys worked for the bike flawlessly? If yes, then I don't have to recommend you to click on the 'Restore Defaults' button in Controller Setup main menu.
If you have a laptop -> make sure you are pressing down on the correct key properly. If you have a desktop -> while holding
onto the [UP] arrow key, hold down onto the  key as well on the numpad simultaneously (some keyboards don't allow you to press down on multiple keys at once). Note: The plane won't take off right away, you need to keep tapping
on the  key while in the water for long periods. Take 2 Support
has info on flying the plane. It's in the FAQ
By the way, this is assuming you have a keyboard and nothin' else like a joystick/gamepad. I heard pressing the [ESC] to get into the main menu and pressing it again, might not allow the keyboard to respond to your commands if you don't try repressing the correct key again.