This is difficult grammar! In your sentence, "being associated with cultivation" is an adjective clause. It modifies the noun "metaphor." To be even more technical, the adjective clause is modifying "it," (which refers to "metaphor"). To show the relationship of these parts, the sentence could be written like this: "You're using a metaphor but that metaphor, being associated with cultivation, doesn't make sense." It is difficult to see the relationship because the adjective clause starts with a gerund (being) and is detached from the word it is modifying. That is a technical description, but I hope it makes sense.

being part of / being compared to / being involved with.