Etymology

color charge

Today it means: In the Standard Model of particle physics, a property possessed by quarks, antiquarks, and gluons that determine rules for how these particles may interact. There are three pairs of colors and anticolors: red, green, blue, and their corresponding anti-colors (e.g. anti-red). Full definition →

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The story

From a loose analogy to the set of primary colors. The charge property has nothing to do with visible color.

Etymology from Wiktionary, CC BY-SA 4.0.