Most prescription medications are highly toxic. The body knows, this, and the stomach gets upset, letting you know not to poison yourself with such things.
Prescription medicines are, by and large, foreign chemicals. For a prescription medicine to be effective, the dose must be high enough to overwhelm the liver, which cleanses the body of foreign chemicals. Only such a high dose will keep the medicine in the body long enough to fight the illness.
Antibiotics are toxic in another way - they kill of friendly intestinal bacteria that help us digest food.
If you must take these medicines, generally, take them with food to avoid stomach upset.
On the other hand, some medicines do not cause stomach upset and are best taken with no food, so they will be absorbed more fully.
Supplements and herbs are a different story. Supplements (such as vitamins and minerals) generally go well with food because they are extra elements of healthy food and will get absorbed better that way. Vitamin C, though, is best taken with just a little natural citrus or tomato, something that contains Vitamin C. That will help with absorption.
Herbs are best taken on an empty stomach, as they are harmless and do not upset the stomach, and will be absorbed better on their own.
Probiotics must be taken on an empty stomach - 2 hours after you eat, and 20 minutes before - to be effective. I take mine when I wake up, and wait 20 minutes before breakfast.