Guilt refers to a feeling of having done something bad or a perception that you did something wrong. Guilt by association means that you personally didn't really do something wrong but that people who you are associated with did. You are judged by the company you keep, so you can be viewed as guilty because of your association with wrongdoers.
There are many examples of guilt by association including:
These are all examples of guilt by association. Any situation in which the perception of a person or idea is colored by the company he keeps or by the source of the idea is an example of guilt by association.