Because he didn't know anything about electrons, and the experiment he did involving rubbing amber and glass rods on fur and silk cloth only showed that something was transferred between the two materials, and that when the material containing the substance was brought near to the other material containing the other substance, the property conferred by the substances appeared to negate. If you read Teaching Introduct…
The reason why which charge is named positive and which is named negative does not matter is because in all the equations that relate electric charge with other measurable physical quantities we never have an electric charge alone, but we always have the product of two electric charges. The value of the product of two electric charges is invariant to the convention chosen for the sign of the electric charge. Numbers…
IIRC a Veritasium video claims that these where essentially discovered by mistake in lightbulbs, so I suspect that Franklin would have had a hard time finding them...