An edge state is a time-harmonic solution of a conservative wave system, e.g. Schroedinger, Maxwell, which is propagating (plane-wave-like) parallel to, and localized transverse to, a line-defect or edge. Topologically protected edge states are edge states which are stable against spatially localized (even strong) deformations of the edge. First studied in the context of the quantum Hall effect, protected edge states have attracted huge interest due to their role in the field of topological insulators. Theoretical understanding of topological protection has mainly come from discrete (tight-binding) models and direct numerical simulation. In this paper we consider a rich family of continuum PDE models for which we rigorously study regimes where topologically protected edge states exist. Our model is a class of Schroedinger operators on $mathbb{R}^2$ with a background 2D honeycomb potential perturbed by an edge-potential. The edge potential is a domain-wall interpolation, transverse to a prescribed rational edge, between two distinct periodic structures. General conditions are given for the bifurcation of a branch of topologically protected edge states from Dirac points of the background honeycomb structure. The bifurcation is seeded by the zero mode of a 1D effective Dirac operator. A key condition is a spectral no-fold condition for the prescribed edge. We then use this result to prove the existence of topologically protected edge states along zigzag edges of certain honeycomb structures. Our results are consistent with the physics literature and appear to be the first rigorous results on the existence of topologically protected edge states for continuum 2D PDE systems describing waves in a non-trivial periodic medium. We also show that the family of Hamiltonians we study contains cases where zigzag edge states exist, but which are not topologically protected.