While existing security protocols were designed with a focus on the core network, the enhancement of the security of the B5G access network becomes of critical importance. Despite the strengthening of 5G security protocols with respect to LTE, there are still open issues that have not been fully addressed. This work is articulated around the premise that rethinking the security design bottom up, starting at the physical layer, is not only viable in 6G but importantly, arises as an efficient way to overcome security hurdles in novel use cases, notably massive machine type communications (mMTC), ultra reliable low latency communications (URLLC) and autonomous cyberphysical systems. Unlike existing review papers that treat physical layer security orthogonally to cryptography, we will try to provide a few insights of underlying connections. Discussing many practical issues, we will present a comprehensive review of the state-of-the-art in i) secret key generation from shared randomness, ii) the wiretap channel and fundamental limits, iii) authentication of devices using physical unclonable functions (PUFs), localization and multi-factor authentication, and, iv) jamming attacks at the physical layer. We finally conclude with the proposers' aspirations for the 6G security landscape, in the hyper-connectivity and semantic communications era.