The exponential growth of information and communication technologies have caused a profound shift in the way humans engineer systems leading to the emergence of closed-loop systems involving strong integration and coordination of physical and cyber components, often referred to as cyber-physical systems (CPSs). Because of these disruptive changes, physical systems can now be attacked through cyberspace and cyberspace can be attacked through physical means. The paper considers security and resilience as system properties emerging from the intersection of system dynamics and the computing architecture. A modeling and simulation integration platform for experimentation and evaluation of resilient CPSs is presented using smart transportation systems as the application domain. Evaluation of resilience is based on attacker-defender games using simulations of sufficient fidelity. The platform integrates 1) realistic models of cyber and physical components and their interactions; 2) cyber attack models that focus on the impact of attacks to CPS behavior and operation; and 3) operational scenarios that can be used for evaluation of cybersecurity risks. Three case studies are presented to demonstrate the advantages of the platform: 1) vulnerability analysis of transportation networks to traffic signal tampering; 2) resilient sensor selection for forecasting traffic flow; and 3) resilient traffic signal control in the presence of denial-of-service attacks.