You can use this phrase to talk about a wide variety of subjects: a group of people, a product, the environment, etc. This means that someone is doing bad things to the subject:

Something horrible is being done to the rainforests.

This means that some people are doing bad things to the rainforests.

We've got to stop what's being done to the educational system in this country.

This means that some people (like maybe politicians) are harming the educational system, and we need to stop that.