Benjamin Franklin proposed electric fluid theory and considered electric current to be flow of a charged fluid. He meant to use positive to denote a surplus of the fluid, negative as a deficit of it. No one knows how he came up with the choice, but it became the convention and as a result lead also to the labeling of charge. I know of no fact that could lead him to that choice. It might just be random. Years later Thompson discovered electron, and according to already established convention, it had a negative charge.
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