A high-fidelity linear time-invariant model of the aero-servo-elastic response of a wind turbine with trailing-edge flaps is presented and used for systematic tuning of an individual flap controller. The model includes the quasi-steady aerodynamic effects of trailing-edge flaps on wind turbine blades and is integrated in the linear aeroelastic code HAWCStab2. The dynamic response predicted by the linear model is validated against non-linear simulations, and the quasi-steady assumption does not cause any significant response bias for flap deflection with frequencies up to 2-3 Hz. The linear aero-servo-elastic model support the design, systematic tuning and model synthesis of smart rotor control systems. As an example application, the gains of an individual flap controller are tuned using the Ziegler-Nichols method for the full-order poles. The flap controller is based on feedback of inverse Coleman transformed and low-pass filtered flapwise blade root moments to the cyclic flap angles through two proportional-integral controllers. The load alleviation potential of the active flap control, anticipated by the frequency response of the linear closed-loop model, is also confirmed by non-linear time simulations. The simulations report reductions of lifetime fatigue damage up to 17% at the blade root and up to 4% at the tower bottom.