I am not a vet, but I do not believe rain rot is a fungus; it is bacterial. It usually appears on their tops, around tail heads, on the top of the shoulders. I have seen it some on the legs and hocks. It will be in areas that are getting wet and staying wet......out in the rain or not getting dry enough if you are blowing the animal out after rinsing or bathing. Cattle with very thick hair are more prone to getting it.
Take a comb and scrape off the loose skin, scabs and loose hair and then shampoo with Betadine Shampoo. You will need to leave the shampoo on for a few minutes before rinsing it off.
You need to rule out lice. Lice can cause hair loss in any area but you notice hair loss the most in areas where the animal can rub against things. You can dust them with louse powder or use a pour on.
The Betadine Shampoo or louse products can be found at TSC.
Hope this helps and good luck.