From the Seattle Times:
The appendix "acts as a good safe house for bacteria," said Duke surgery professor Bill Parker, a co-author of the study. Its location — just below the normal one-way flow of food and germs in the large intestine in a sort of gut cul-de-sac — helps support the theory, he said.
Also, the worm-shaped organ outgrowth acts like a bacteria factory, cultivating good germs, Parker said.
That use is not needed in a modern industrialized society, Parker said. If a person's gut flora die, they usually can repopulate it easily with germs they pick up from other people, he said.
But before dense populations in modern times and during epidemics of cholera that affected a whole region, it wasn't as easy to grow back that bacteria and the appendix came in handy.