Pathogens and non-pathogens are not alike, as one is a type of bacteria/illness inside your body when a non-pathogen is not inside your body and it is not an illness or a bacteria.
A pathogen is a microorganism which is able to cause diesease or illness in a human being or other animal. A non-pathogenic microorganism does not cause disease or illness.
A non-pathogen is an organism that is not pathogenic. i.e. does not cause disease. Examples would be many of the organisms that reside in your intestines.