Not very natural but I had good luck with Boudreux's (sp?) Butt Paste when DD had a red, tender rash. Usually, though, she tended towards yeasty rashes instead, in which case clotrimizole (Lotrimin) worked very quickly.
And it is tough to do especially as weather gets colder but lots of nekkie time. You can also try drying the diaper area with a hair dryer on low setting after washing him and before putting on the diaper cream and new diaper.