Some of the problem with weeds is the context. For example weeds near a river could dominate the soil and make it unstable or dehydrated, affecting the water supply. Fennel is considered to be a problem for this if it grows near a river bank. However fennel itself is not harmful. It contains many nutrients and is a healthy food for humans. If we were to remove fennel from the riverbank and eat it we are an effective part of the ecosystem and everything benefits. But we tend to destroy and control rather than make good use of a plant that is in the wrong place.
(adapted from an online article about weeds I wrote for Frowned Upon)