The "bean" is a waxy buildup for gunk that settles in his penis. If left unchecked, it can cause alight discomfort or extreme pain.
I clean my geldings every 6 months after a good workout. Use rubber gloves, LOTS of KY and warm water and get in there. it's gross but for their health, it needs to be done. if it grosses you out buy a nice natural sheath cleaner, spray it up in there and it will take care of itself (mostly, you'll still need to loosen stuff off for him!)
My vet told me horses in the wild "use it" so it helps flush them out a little, but it does not make them any less prone to diseases and such ;)