A robust adaptive type-2 fuzzy logic controller is designed for the longitudinal dynamics of a flexible air-breathing hypersonic vehicle. The aircraft's pitch motion and flexible vibration are strongly coupled explicitly in the dynamic equations. The throttle setting is designed to control the velocity by dynamic inversion control method. The elevator deflection is designed to stabilize the pitch rate and flexible modes and in the end control the altitude in a stepwise manner by backstepping control method. The flexible modes are actively used in the control design in order to counteract both the tracking errors and the flexible vibrations. The virtual control signals in backstepping control as well as their derivatives are obtained by command filters whose magnitudes, bandwidths and rate limit constraints can be set. The transition processes of the velocity and altitude commands are also obtained by command filters. Uncertainties are estimated online by interval type-2 adaptive fuzzy logic system. The adaptive law of the fuzzy logic system is derived by Lyapunov synthesis approach. Simulation results demonstrate the effectiveness and robustness of the proposed controller and also validate type-2 fuzzy logic is more capable of handling uncertainties than type-1 fuzzy logic.