This paper addresses the problem of autonomous transition between hover and level flight for a model-scale fixed-wing Unmanned Air Vehicle (UAV). The UAV system is described as a Hybrid Automaton where the different operating modes correspond to the hover, transition, and level flight regions of the flight envelope. Reference maneuvers are generated so as to provide robustness to the system with respect to exogenous disturbances and parametric uncertainty when performing single operating mode and transition maneuvers. Controllers rendering the closed-loop system Input-to-State Stable (ISS) with restrictions are designed for all three operating modes allowing for practical tracking of the reference maneuvers in the presence of disturbances. Simulation results demonstrate the performance and robustness of the proposed solution.