Automatic-dependent systems are vital to air and maritime traffic control and play a key role in maintaining global transportation networks’ safety, efficiency, and coordination. Cyber attacks on these systems can result in significant disruptions to global transportation. In this study, we thoroughly review the cryptographic, security, and privacy schemes proposed to protect Automatic Dependent-Surveillance Broadcast (ADS-B) and Automatic Identification System (AIS) systems and a comprehensive map of potential attacks based on security requirements. This study outlines the security requirements necessary to protect these systems from cyber attacks and identifies the possible vulnerabilities that could be exploited. Through a comparative analysis of the proposed schemes, we provide an overview of their advantages, limitations, and compatibility with existing protocols and message formats. Our study aims to assist researchers and practitioners in understanding and enhancing the AIS and ADS-B ecosystems by providing effective, compatible, and cutting-edge hardening solutions.