Straight from the doctor's mouth! How to soothe your stomach when taking antibiotics:

Many patients tell me that when they take antibiotics they get an upset stomach or diarrhea. So whenever I prescribe antibiotics, I recommend that they also add yogurt to their daily diet to prevent stomach disorder.

The intestines have a variety of good bacteria that aid in digestion.  Antibiotics can kill a significant number of those good bacteria.  Yogurt has live active bacterial cultures that can keep the intestines happy and healthy while taking antibiotics.  Patients should eat a variety of different yogurt brands for the most beneficial effect. 

Take the yogurt about 2 hours after each antibiotic dose.