Control variables serve as the inputs to the simulator. The user has more or less complete control over the values; the simulator sets these variables based on input from the user. For example, if a control stick is attached to the simulator, the simulator sets the elevator deflection variable to correspond to the stick's position.
The basic airplane control variables include the aerodynamic surface deflections (elevator, ailerons, rudder, and flaps), and the engine controls (throttle, blade pitch, mixture). Other control variables include the brake pressure, trim tab deflections, the position of the landing gears (retracted, extended, or in transition), whether carburetor heat is on, etc. There are far too many to list.
Even some values which are not normally considered to be controls can be control variables. For example, payload mass is a variable directly controlled by the user, and so the flight simulator considers it a control variable.
Note that there is no requirement that a particular variable be of a certain type. A quantity could be a control variable in one flight simulator, and a state variable in another. For example, a flight simulator could treat force on the control stick as the control variable, with the control surface deflections being state variables. (This is a convenient way to model stick-free flight.) Some engines have governors on them the fix the RPM; in this case, the RPM is a control variable while the blade pitch is a state variable.