Your professors try to oversimplify things because there are few ways to describe the host-parasite relationship in symbiosis. Sometimes it is mutual, most of the time commensal, and we concentrate on parasitism. Unfortunately, they are not distinct and things are fluid. So most of the time the bacteria/viruses have evolved in certain ways to not cause mortal disease in humans as that blocks their transmission. The disease process is usually a means to spread to other areas where they can evade immunity. Most of the time this only occurs when the hose is immunocompromised and cannot contain an infection. (Think TB and granulomas). The most successful human infectious agents infect a vast majority of the population, become closely associated with host cells, and can lie dormant for a lifetime. They can also easily spread. Things that come to mind are HPV and HSV. Then there is the normal flora that mind their own business and love fermenting things that we can't digest. They may give us some useful vitamins like K but they also have antigens that sensitize us to other blood group antigens or produce autoimmunity.
By the way, GiantMicrobes are the best. I have a bunch, but back in undergrad I told my micro professor my girlfriend gave me syphilis and gonorrhea and he didn't know what to think. I had to reassure him that I was talking about GiantMicrobes. (This was after I gave him an E. coli as a gift but he was still confused about the idea).
