Aircraft with internal carriage of weapons systems require active control strategies to limit high amplitude open bay acoustic resonances and to optimize structure requirements and weapon reliability in an enlarged separation envelope. This paper is focused on communicating an investigation into the use of numerical simulations combined with Proper Orthogonal Decomposition (POD) to optimize an active control system for an aircraft weapons bay application. Issues addressed include characterizing shear layer and wake resonant responses, optimal steady blowing rates, the effect of open loop harmonic perturbations, use of POD for post processing data to reduce storage requirements, and the use of the Nelder-Mead optimization procedure. Comparison of the wake and shear layer responses shows why no aircraft would ever want to experience a wake response. This study intends to develop flow instability suppression strategies that may be scalable for implementation in a weapons bay application. A lower Reynolds number flow is considered here, which can be modeled numerically with the computational resources currently available. As the essential flow physics of some cavity instabilities are mainly inviscid, it is expected that control techniques for the shear-layer instability mode may be reasonably scaled. This work focuses primarily on a freestream flow at M=0.85 with a cavity of aspect ratio L/D = 4.5. The results include the use of steady blowing injection up to M = 0.9 and harmonic forcing perturbations ranging in amplitude from M=0.005 to M=0.45. In the parameter space examined mass injection (displacement effect) has the largest effect and momentum considerations are minor. The best observed forcing reduced the buffet loading metrics by approximately 17 dB.