A saddle fitter said that ingrown hairs (due to friction of the saddle) had caused a horse at the barn to develop raised, round 25 cent coin sized bumps under the horse's saddle area. These particular bumps weren't sore looking, no hair loss, raised and quite round in shape. No scabbing, oozing or noticeable injury to the skin/coat.
If they're small hard bumps that don't cause any pain when you press on them have your saddle refit. My horse had these. When the saddle was fitting well they went away. When they came back I knew I needed to get my saddle fit again- I think they are caused by friction from the saddle moving.
Call your veterinarian if an infection fails to improve after a week, despite treatment. He can make sure your horse actually has rainrot, rather than another similar condition, and may prescribe a topical medication or oral antibiotics, especially if a secondary infection has set in.
First remove the horse from wet conditions and place him in a living arrangement where his coat can dry out thoroughly. A variety of anti-microbial shampoos and disinfectant rinses are available over-the-counter that are labeled for use on rainrot infections; the horse's coat will probably need to be treated daily for at least a week. The specific duration of treatment depends on the product being used and the severity of the infection. Spot treating may be effective if only a small area is affected; otherwise, giving the horse a full bath may be advisable.