We present a method to design controllers for safety specifications in hybrid systems. The hybrid system combines discrete event dynamics with nonlinear continuous dynamics: the discrete event dynamics model linguistic and qualitative information and naturally accommodate mode switching logic, and the continuous dynamics model the physical processes themselves, such as the continuous response of an aircraft to the forces of aileron and throttle. Input variables model both continuous and discrete control and disturbance parameters. We translate safety specifications into restrictions on the system's reachable sets of states. Then, using analysis based on optimal control and game theory for automata and continuous dynamical systems, we derive Hamilton-Jacobi equations whose solutions describe the boundaries of reachable sets. These equations are the heart of our general controller synthesis technique for hybrid systems, in which we calculate feedback control laws for the continuous and discrete variables, which guarantee that the hybrid system remains in the safe subset of the reachable set. We discuss issues related to computing solutions to Hamilton-Jacobi equations. Throughout, we demonstrate out techniques on examples of hybrid automata modeling aircraft conflict resolution, autopilot flight mode switching, and vehicle collision avoidance.