Cyber-security has emerged as a pressing issue for transportation systems. Studies have shown that attackers can attack modern vehicles from a variety of interfaces and gain access to the most safety-critical components. Such threats become even broader and more challenging with the emergence of vehicle-to-vehicle (V2V) and vehicle-to-infrastructure (V2I) communication technologies. Addressing the security issues in transportation systems requires comprehensive approaches that encompass considerations of security mechanisms, safety properties, resource constraints, and other related system metrics. In this work, we propose an integrated framework that combines hybrid modeling, formal verification, and automated synthesis techniques for analyzing the security and safety of transportation systems and carrying out design space exploration of both in-vehicle electronic control systems and vehicle-to-vehicle communications. We demonstrate the ideas of our framework through a case study of cooperative adaptive cruise control.