This paper discusses the development of a control architecture for hybrid Unmanned Aerial Vehicles (UAVs) based on model-free control (MFC) algorithms. Hybrid UAVs combine the beneficial features of fixed-wing UAVs with Vertical Take-Off and Landing (VTOL) capabilities to perform five different flight phases during typical missions, such as vertical takeoff, transitioning flight, forward flight, hovering and vertical landing. Based on model-free control principles, a novel control architecture that handles the hybrid UAV dynamics at any flight phase is presented. This unified controller allows autonomous flights without discontinuities of switching for the entire flight envelope with position tracking, velocity control and attitude stabilization. Simulation results show that the proposed control architecture provides an effective control performance for the entire flight envelope and excellent disturbance rejections during the critical flight phases, such as transitioning and hovering flights in windy conditions.