According to the Merriam-Webster Dictionary, "non-pathogenic" means that an organism does not cause disease, so non-pathogenic bacteria do not cause illness. Some bacteria are helpful within their environments.
For example, the human digestive tract contains bacteria that help it function properly. These bacteria not only aid in the digestive process, they also kill pathogenic bacteria. Bacteria are used in the production of certain dairy products, such as cheese, sour cream and yogurt. In the natural world, some bacteria function as decomposers, breaking down dead organisms. Other types of bacteria consume oil, and this natural tendency is most visible during oil spills or leaks.