Your doctor may want to go back and review his Latin. The word,
acidophilus, means acid-loving, and these particular organisms survive stomach acid quite well. Many other species also survive quite well, including Bifidobacterium lactic (have attached an article to show your doc). As with other aspects of the human body, there are great differences among individuals as to what their microflora population consists of, due to age, which types the diet provides, gastric acidity, whether the diet otherwise supports their proliferation, and what specific strains an individual starts life with.
Also, following the same logic, no one should be able to be infected with E. coli or salmonella, since stomach acid should kill them. Many folks have inadequate acidity and sometimes the sheer number of organisms entering the body can overwhelm the mechanisms to keep them out. Bacteria are sneaky.
I suggest the following reference as an excellent article on human microbiota as they actually exist in the gut. It doesn't specifically address how they survive transit, but it does an excellent job of explaining the intricacies of their lives in our bodies: Reuter, G. (2001). The lactobacillus and bifidobacterium microflora of the human intestine: Composition and succession. Current Issues in Intestinal Microbiology, 2(2): 43-53. Retrieved from
http://www.open-access-biology.com/probiotics/reuter/reuter.html