When you ride, are you using a cycling-cream, like DZ-Nutz or Chamois Butt'r? You can be chaffing from the shorts shifting against your skin. I prefer to use Shea Butter but have used Chamois Butt'r and it works well too. I've never had an issue with saddle sores and rashes once I started using them.

I also like to soap down that area with Hibiclens soap to take care of any bacteria from sweating, after my rides. It is also good to have around in case of road rash, it's great for scrubbing out wounds. Tea-Tree oil is also good for things like saddle sores (and for cleaning up poison-ivy, I've heard). So I keep some around, as we have plenty of poison-ivy where I MTB.