Think this one through logically.
Staying dry: Most modern cycling shorts have a coolmax pad. It's designed to wick moisture away from the body. It works because when you sweat it actively makes the moisture come away from your skin, so your skin stays dry. Because it is a manmade wicking fibre, it does not absorb the moisture, so it stays relatively dry. If you then put a layer of cotton underwear between the pad and your skin, any moisture is absorbed by the cotton fibres, and stays there, to be transmitted back onto your skin. Wearing cotton underwear between pad and skin therefore defeats the object of the wicking properties of the pad.
Chafing/pressure/soreness. The pad is soft, held in place from all directions, moulds to your body/undercarriage, and takes the brunt of the movement between saddle surface and undercarriage. If you add another layer between the two, it shifts and gathers, leading to chafing and sores.
Hygiene/Odour. Sorry all, but modern coolmax pads are often anti-bacterial. They are constructed using silver, which itself had medically proven antibacterial properties. Body odour occurs when perspiration is eaten by bacteria, and the by-product of their feast is a smelly concoction of gases. If the bacteria are discouraged from feasting on perspiration by the coolmax properties, it stands to reason that the odour will be lessened. If you then wear an absorbent layer between the pad and sweat glands, it creates a reservoir of sweat, the bacteria attack it happily, and odour results.
Creams and ointments. I am a big bloke and sweat a lot when I exercise. If however I shower before I ride, and smear sudocrem on my undercarriage, it has two effects. Firstly it stops chafing, as the skin is lubricated. Secondly, the zinc oxide in the cream has a anti-perspirant effect. If I then wear a good quality pair of shorts, with a coolmax silver pad next to my skin, I can honestly say that no matter how hard I ride, the pad remains fresh (ish)