This is what I've learned from word-of-mouth: Plenty of them die, but some of them make it. They're hearty little bugs, and they also reproduce very fast (as all bacteria do). So even if only a few make it, they can quickly populate your gut from the luckiest/toughest survivors.
Commercial strains of probiotics aren't as tough; they're living in processed foods and/or have been heavily processed themselves, and so are weak by the time you bring them home and eat them. That's why probiotic supplements need help in the form of encapsulation. I've also read that commercial yogurts and kefirs often cannot deliver on the promised probiotics because the bugs just cannot survive.
I don't have actual research links. But I know that kefir is doing something in there -- when I drink too much at once, I sure know it. Some pretty epic bacterial battles occur when I send in a ton of troops!
Edit to provide an interesting quote from Wikipedia:
"Both kefir and yogurt improve lactose digestion simply because some of the bacterial cells give up their lives in the intestinal tract, release their enzymes and digest the lactose. It's a one-shot deal. However, kefir has additional microorganisms that may be able to colonize the intestines and benefit health further by protecting the intestine against disease-causing bacteria." -ScienceDaily. 2003-05-30.
...so they are making it to your intestinal tract, but most of them die there; however, kefir has so many types of bacteria that some types just might take up residence and keep helping you out.