So, when Ben Franklin named them, it was in terms of something like "excess of electricity". A positive excess of charge, like in the glass he used to define the term, is actually a deficit (negative excess) of electrons, which are the real fluid.

Later on Crooks (I think?) figured out that if he cleared all the air out of a tube with mercury, he could force electrons out of the metal into open space, at the negative cathode end, and at that point they realised it was backwards.