Flies, much like roaches, only infest when there are food/water sources available. Despite what you may have witnessed at your least favorite fast food store; flies are not commonly found in good restaurants and must be dealt with immediately, once you notice a problem.
One common solution is to spend a little more time outdoors, and keeping the external parameter clean. If you still have a problem with flies then you may want to think about investing in heavier doors, to reduce the amount of time the door stays open, as well as indoor flytraps. However, fly zappers are not considered hygienic in restaurants. The best flytraps use ultraviolet technology and pheromone attractant. Luralite, Maxforce, Vector and Cento all make flytraps products.