This paper addresses the trajectory tracking problem for VTOL UAVs in which the thrust vector can be delivered only in a fixed direction with respect to the aircraft frame. The proposed control law, based on an inner-outer loop strategy, guarantees robust tracking of a desired position trajectory. The attitude error dynamics, associated to the inner loop, is stabilized by a control torque that does not cancel non-harmful nonlinearities and that tracks at the same time a desired heading direction. This choice results in a non-autonomous feedback interconnection between the attitude and position loops, the stability of which is studied within the framework of differential inclusions. The proposed control force accounts for attitude errors to improve transient performance compared to other designs. The control scheme is tested on a multi-body model of a hexacopter UAV with actuators dynamics and aerodynamics effects, not included in the control design model.