They will X-ray all your stuff, they may check them more closely - by just a random pick or if they are suspicious for some reason. That will probably tell more about you than what your genitals look like (chances are they are just typical normal genitals).
If they think you might have some narcotics stuck in your ass, they will physically intrude your body to try and find them.
Since you can put only a fraction of passengers through the scanners, the real problem is that how you use them scanner. It may be a real humiliation to the people picked. So, you cannot pick by race, religion and stuff like that. Random? - Okay but doesn't really stop any terror attempts. Maybe you are on some CIA watchlist, which doesn't necessarily make you a terrorist, but other passengers will think you may be a terrorist, even if you ware picked by random.