Motivated by recent interest in simulations of hypersonic flows under re-entry conditions, a robust and accurate shock capturing approach for high-order discontinuous Galerkin methods is developed. Artificial viscosity is localized via a shock detector based on the entropy residual, which converges to zero in smooth regions and assumes nonzero values in non-smooth regions. The piecewise-constant artificial viscosity field is then diffused in order to generate a smooth profile to avoid spurious oscillations of the solution near the shock (Barter and Darmofal, 2010). To improve accuracy, this method is combined with mesh adaptation and a procedure for optimizing the artificial viscosity field. The performance of this approach is investigated in numerical tests of hypersonic flow over 2D and 3D cylinders. Results concerning heat transfer predictions demonstrate that this shock capturing scheme is relatively insensitive to errors caused by misalignment between unstructured meshes and the shock.