The HEPA filters are similar to the ones found in operating theatres. The difference is that the operating theatre will typically have it's air changed about every twenty minutes whereas an airliner typically replaces the volume of air in the cabin in about twelve. The air is quite clean and added to the fact that many pathogens have a problem surviving for any length of time in the dry atmosphere of the cabin, it's more likely you picked up your bug from the person next to you, or at your destination, for which you may not have strong immunity against the local pathogens.