Human beings do a large variety of very strange things with sexual organs, either our own or those belonging to other species. Consider that we often give the severed sexual organs of various plants to our significant others, the predilection that some have for rocky mountain oysters, or the rather severe taboo on displaying these parts (on humans) that prevails in many Western societies. We use the term "private" to describe such parts, owing to the cultural mandated ban on public exposure. There are certainly very good explanations for all of these behaviours. Many of those explanations are evolutionary in character and some have only been recently understood.
The cutting of genitalia, especially in the very young, is a cultural practice that is widespread amongst Abrahamic religions. It is yet another behaviour that admits an evolutionary explanation as Connor Wood explains on his blog Religion and Science: