Question

why didn't natural selection lead to evolution of totally harmless parasites?

Answer 1

Natural selection generally doesn't favor totally avirulent parasites (that is those which are totally harmless) because there is often positive association between virulence and transmissibility...... So, if virulence goes down, so does transmissibility---such strains will have lower fitness. That's why natural selection didn't lead to evolution of totally harmless (avirulent strains) parasites.

Answer 2

Natural selection didn't lead to the evolution of totally harmless parasite because if a parasite becomes totally harmless, then it is not parasitism but commensalism.