If microbes have coevolved with our species ( sapiens) why are so many of these relationships parasitic?

I don't understand the "if-then" nature of the question. Many microbes parasitize humans specifically because they coevolved with them and are thus able to counteract human defenses to at least some extent. Are you wondering whey humans haven't evolved better defenses? For one thing, humans evolve more slowly because their generation times are longer. For another, it's not usually in the microbes' best interest to quickly kill the host human, so they tend to evolve so as to avoid that. That leaves the host human with less evolutionary pressure to evolve completely effective defenses. And any near-completely effective defenses humans did evolve would present strong evolutionary pressure on the microbes to overcome.