The organisms in nature are all parts of a complicated interplay, where all "parts" have their function for the whole. Plants "catch" energy from the sun and make it available for other species. At the same time they produce the oxygen that all other species depend upon. Some species eat plants and are themselves being eaten by others. Many insects contribute in pollinating flowers. Insects and their larvae are important food, for example for fish. Many fungi and bacteria are specialized in decomposing dead animals and plants so that the nutrients can be used again.
If an organism is being removed from this complicated system, it can have a large effect on the rest of the system. If the capelin disappears from the Barents Sea , we know that this will lead to a collapse in the populations of cod, seabirds, seals and many other organisms. This knowledge is gained through hard experiences. For most organisms we do not know the effect if they disappear from nature.
On the other hand, we know that humans are totally dependent on the interactions in nature in order for us to gain food, clean water and fresh air. Therefore it is in our own interest to protect nature.