DISCLAIMER: I am not a doctor, but am good at researching things.
According to most web sites I've looked at, there could be many reasons why the skin is peeling:
Allergies to lubrication products (KY Jelly for example), or lubricated condoms, or even a latex allergy.
Allergies to the females natural lubrication.
Too much sex, i.e. friction burn.
Use of "desensitizing" products will also cause skin peel.
There is not a Sexually Transmitted Disease that will cause skin peeling, so don't be worried there. Genital herpes MAY cause peeling, but there will be painful bumps and sores first.
Exposure to a yeast infection can also cause peeling skin in men.
If you use condoms, I would try a non-lubricated, or natural (sheepskin condoms) and see if that helps. Or try not having sex very frequently.
I hope this information can help.

