Whilst many organisms are purely pathogenic to humans (disease causing) and the severity of illness depends on host factors, there are also organisms that are usually commensal (colonise the host without causing disease), but under certain conditions, can become pathogenic. Examples are some of the streptococci bacteria and candida fungi that normally colonise our skin & mucosa.
Conditions that cause these usually benign organisms include loss of skin & mucosa integrity as zizi2003 has already described, the host becoming immunosuppressed or immunocompromised due to immune system dysfunction, HIV infection, chemotherapy dugs etc, as well as disturbances to the balance of species of organisms, such as killing off of other protective organisms by antibiotics.