There are many theories regarding germs and their role in disease. The germ theory was first postulated by Louis Pasteur, and Robert Koch extended his observation into a discovery of large (yet false) medical significance. In homeopathy germs are not viewed as the primary cause of disease. Based on the vitalistic approach disease is related to the decrease in vital energy, and if this has reached a certain low level the patient becomes susceptible to infections.
There is another theory suggesting that each disease is biphasic, beginning with the permanent sympatheticotonia to be followed by the permanent vagotonia in which pathogens appear and even support the body in it's recovery of health - suggesting that microbes are not the cause but consequence of disease.
If interested, please read this article critically and let me have your comments !