We're actually in the infancy stage of understanding the gut flora microbiome. From the casual research I've done of scientific articles, a lot of the benefit of probiotics comes from the fatty acids and other metabolites they produce. When you eat something like yogurt where they've been cultured, you get all these products with it but in a capsule all you get is the bacteria itself. Given the hundreds of species of probiotics that inhabit the gut, taking a single-strain like Acidophilus may one day seem as bizarre as only eating one single food and expecting it to meet all your nutritional needs. It's unfortunate but there's just not enough yet known about how it all works. It's basically a guessing game for now.