Increasingly ambitious robotic and human entry missions at Mars will likely require advances in entry guidance, navigation, and control for mission success. Articulating aerodynamic flaps are a potential alternative to bank-angle steering that provide nearly independent control over angle of attack and sideslip angle, possibly enabling improved flight performance. In this study, a general flap controller is designed to accommodate arbitrary blunt body flap configurations using nonlinear model predictive control. Performance is assessed for a variety of commands, including step responses and simulated guidance commands over an entire trajectory. Metrics such as response time and tracking are assessed. The controller was found to provide good performance for different flap sizes, numbers of flaps, and flap locations on the vehicle. The settling time was found to be the lowest at moderate dynamic pressures on the order of 5 kPa, and a single controller was able to accurately track angle of attack and sideslip angle commands with time-varying dynamic pressure and Mach number, without gain scheduling. Comparison to a linear-quadratic regulator controller shows that the model predictive controller has both improved settling time and tracking performance, relative to the linear-quadratic regulator, at the expense of increased computational resource requirements.