Most games operate in two dimensions. Mice go up and down and side to side.
Joysticks can go left and right and up and down.
Think about a square versus a cube. Traditional controllers can move you around the square but can't handle navigation of the cube. Flight and space sims give you the illusion of navigating three dimensional space by twisting the square. The best way to understand how to take advantage of this concept is to think about playing Quake with a mouse and a keyboard. The keyboard arrows provide the direction control while the mouse handles your view point.