A more precise expression would be, "We kill everything that we imagine competes with our interests and well-being".
We kill insects that help themselves to a portion of our crops, by spraying the crops with poison. We shoot or trap certain birds and other wildlife that might naturally try to feed themselves on our crops.
We kill countless bacteria in the interests of hygiene, including bacteria which are beneficial to us, simple because there is a false impression that all bacteria are bad, and so on.