Rubbing as in abrasive to your skin and you are getting a sore rubbed in to it? Or is this some numbness or muscle pain?
If it is abrasive rubbing and this is on a road bike, then do you wear snug fitting bike shorts or bibs sans underwear? If so then maybe you need to groom down there to make the hair a little shorter. Too much hair just rolls around like little roller bearings between the skin and fabric of shorts. That gets irritating quick for me and it has to go.
Might still be you need to adjust the saddle position slightly fore/aft or tilt.