Wireless sensors and actuators connected by the Internet-of-Things (IoT) are central to the design of advanced cyber-physical systems (CPSs). In such complex, heterogeneous systems, communication links must meet stringent requirements on throughput, latency, and range, while adhering to tight energy budget and providing high levels of security. In this paper, we first summarize wireless communication principles from the perspective of the connectivity needs of IoT and CPS. Based on these principles, we then review the most relevant wireless communication standards before focusing on the key security issues and features of such systems. In particular, the gap between the security features in the communication standards used in CPSs and IoT and their actual vulnerabilities are pointed out with practical examples and recent attacks. We emphasize the need for a more in-depth study of the security issues across all the protocol layers, including both logical layer security and physical layer security.