There's several ways to generate cash. You can sell damaged weapons at the scrap merchant. Also, there is a weapons buyer (only available in full version). Also, if you help Ben Dabi militia in a battle, they may offer to trade weapons for cash. You should also manage spending frugally. For instance, it's not too wise to send soldiers to hospital when they are only down to 80% health - wait til they get down to 60% (you are charged the same rate either way). Also, avoid spending money on repairing weapons that are only marginally better than the ones you already have.