Saddle sores are actually caused by friction between your bottom and your shorts and there are solutions to make your ride more comfortable.
A saddle sore is a skin ailment on the buttocks due to, or exacerbated by, cycling on a bicycle saddle. It often develops in three stages: skin abrasion, folliculitis (which looks like a small, reddish acne), and finally abscess. Because it most commonly starts with skin abrasion, it is desirable to reduce the factors which lead to skin abrasion but also treat any chafing against infection. The best answer to this problem is Chamois Cream, which reduces friction against with your cycling shorts and should contain anti bacterial products to prevent infection.
Other details you can take into consideration are:
Correct fitting of your bike
Do not wear underwear with your cycling shorts..
A decent saddle
A good Chamois Cream reduces friction and keeps your skin cooler. It prevents inflammation and has antibacterial properties. Apply directly on the skin (avoid intimate areas) before each ride. You can also apply a thin layer onto the shorts insert. This will maintain suppleness, elasticity and antibacterial properties.