It simply means that the game controls are not bound to match your hotas ..there's loads of tutorials on YouTube.
But if you use voice attack you can actually get it to do a lot of the keybinding for you.
There's no set way to do it though, it's a lot down to personal preferences as to which button to do what.
But for example if you wanted to bind L to the landing gear , press esc,/ options/controls , scroll down to to misc / landing controls, suggest you use L key as a toggle switch to raise or lower the landing gear . I actually use a misc thruster landing thrusters, so when the gear is down, my lateral and vertical thrusters do the fine movements needed.
That's just one key of about 30 you may need to do....it's a huge time soak but much needed to be able to actually learn to fly your ship....it took me about 3 weeks of messing.
I use a thrustmaster T16000M and wouldn't be without it...if you're struggling , I could send you a copy of my keybinds, if that would help, pm me your email address with a reminder , it will get you started