I lived in Florida so rain rot was a constant problem there. The best solution I found was always using a shampoo like micro Tec (my favorite} Whether permitting I bathe my horses after each ride or weekly for the retired boys. I also have had to treat the back of the foot for scratches by using medicated shampoo followed up with a good smear of desitin(not generic brands}this will soften the scabs so they fall of and it heals underneath. The desitin also keeps them waterproof to avoid recurrence. This was remedy I learned from someone on the race track, I has worked well for me. Micro Tec also makes a spray for when you cant bath them. The other thing about rain rot is by the time you see it the problem is already rooted so prevention is the way to go.
MTG also helps, its a ointment that you can pour on and rub in, it doesn't need to be washed out. Also spraying Listerine on the saddle pads and bits kills the germs.