There are most likely two things going on here. The pain was from a diaper rash and at his age they cling to a fear of pain dearly. Sometimes it comes in some form interfering with potty training or sometimes bath time.
They are intense with these short term memories. Some children can be put into a bath at the wrong temperature and the effect lasts a very long time.
Another thing is, it could be is an Anal Fissure, Of course, I can not diagnose that here. But, I have had many children at this exact age suffer from one of these and their parents not know.
One of the signs is the fear of sitting in a bath because it hurts. Here is a link to tell you more about them and you could get him checked just to make sure.
This can sometimes happen during potty training or even with a child that is very trained.
They are small and you may not be able to see them with your eyes, and can sometimes be internal.
Since he has never shown a fear of water, there is most likely something going on with a pain association.
Yes, there is something going on there. If he has suffered from constipation recently that could also cause tiny tears.
The great news is, this is all treatable. You can have him checked by his doctor and it will have to heal. The best thing to do is assure him you will not let the water get there and try to use a wipe with witch hazel on it to soothe the area.
I have seen children become so scared of potty time that they would scream when going into the bathroom just because ONE time it hurt. They just cling at this age. But, you are correct. You have to clean him.
So as a mother, I understand. My daughter just simply had a fear of water. Yes, I understand. You can look for home remedies, like maybe a soak in the tub that will help, let me see if I can find one for you.
here is some info
like I said, of course, I am only going on experience here. But, this is usually what it is when they do not want their bottom to touch the water...Or like I said, it just hurt when he had the rash. But, the way you describe it, the way he pulls up when the water touches the area, seems like pain may still be present.
I wanted to share this info because many parents will try to examine and as you can see in three...this can worsen the issue.
I would stick with maybe a sitz bath treatment until you see a Doctor. But, most likely before you do, it will heal on it's own.
He may just be uncomfortable with the way it feels. With children this age, they change like the weather. Something that is ok one day can change the next. You letting the air hit it, was the best thing. Just let him wear what he is comfortable with, they will begin to show their preferences at this age.
I would not force the issue. Making the water a little less warm can help. But, then, he may be uncomfortable with that.
If you make him a sitz bath, try something new like tub chalk or something of the like so that he will be distracted by this activity and be soothed at the same time.
Oh, well good, then you are so on the right track. Yes, anything that will pull him from the thought of sitting in the water. New things will distract easily.