As we approach the 6G era, establishing a trustworthy 6G system design is imperative to meet the complex security and privacy challenges, especially those posed by advanced technologies such as joint communication and sensing and AI. This tutorial explores the possibility of rethinking security protocols from the bottom up, with a particular focus on the often-overlooked physical layer. While past generations of mobile networks, from 1G to 5G, have transformed communication, they have also exposed vulnerabilities in security, privacy, and trustworthiness that require special attention. This tutorial introduces the unique challenges presented by the access network and advocates for a holistic security approach that encompasses all the network layers. Key topics of interest include the concept of trustworthiness, the importance of security and privacy in the 6G era, the implications of joint communication and sensing technology, the existing physical layer security principles, including wiretap-coding, secret key generation, and device authentication, and strategies to combat sophisticated attacks. By embedding security principles across the network architecture, attendees will gain insights into a trustworthy wireless system design. This tutorial aims to equip participants with the fundamental knowledge to navigate through the complexities of 6G and contribute to developing trustworthy and resilient 6G systems.