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 Introductory Physics the author very clearly points out that there is no way of knowing the direction of the charge. It must instead be decided by convention. And Franklin simply chose a convention that we stick with.
This is where the need to use mathematical formalism to describe physical concepts becomes clear. Numbers and numeric quantities aren't a real thing that exists in the world. They exist only in our minds. And so does the concept of negation. Calling electrons "negative" is simply a tool for us to model how the substance behaves when it interacts with an "opposing" substance using numbers. We could just as easily have called it "black" or "white" charge, except that we then need to adapt arithmetic and algebra and calculus and so on to work with the concept of "black" or "white" quantities if we are to use them to understand the substance of charge.
This is where the need to use mathematical formalism to describe physical concepts becomes clear. Numbers and numeric quantities aren't a real thing that exists in the world. They exist only in our minds. And so does the concept of negation. Calling electrons "negative" is simply a tool for us to model how the substance behaves when it interacts with an "opposing" substance using numbers. We could just as easily have called it "black" or "white" charge, except that we then need to adapt arithmetic and algebra and calculus and so on to work with the concept of "black" or "white" quantities if we are to use them to understand the substance of charge.