My daughter had the same problem at 2-3 weeks of age. The diaper rash got to be so bad that we had to take her to a pediatric dermatologist. Here is what she prescribed. Brew a stockpot's worth of strong chamomile tea and chill it to a bit cooler than room temperature. Pour some into the baby's tub and soak his little bottom in it for 20 mins, 4 times a day. Yes, the tea is cold and the baby won't like it one bit. However, my daughter was screaming through every diaper change anyway because she was so very raw so you pick your evils, I suppose. Apply a thick coat of Desitin at every diaper change. You should see a marked improvement in 2-3 days.
It works!! My daughter has very sensitive skin, so any bout of diarrhea resulted in diaper rash until she was toilet-trained. Chamomile tea solved the problem every time. The rationale is the following. Cold chamomile is one of the most drying substances in nature, which helps the body to form a protective crust over the affected area.
If your son develops a fungus, characterized by a white substance that won't wash off your son's bottom, you will need to get a prescription for an antifungal ointment from his pediatrician.
Good luck and please feel to email me with any questions.