According to http://www.customprobiotics.com it depends on your goal.
How you use a probiotic depends on why you are taking it. If the primary purpose for taking the probiotic is to aid digestion, then you must take it with meals. If the goal is to have the probiotic reach the lower intestinal tract, then it may be more appropriate to take it between meals, with a full glass of water. Water dilutes the stomach acids and moves the organisms quickly into the intestinal tract. Probiotics can also be used for both purposes by taking some with meals and some between meals.
This totally makes sense if you ask me!
Our ancestors would have gotten their probiotic flora when they ate food so I am of the belief that you should always take probiotics with food. Not sure if there is actual research that supports that but it just seems most natural to me.
Probiotics and Antibiotics 5 Answers