PhysicistsParticle physicists (such as they were in the 1700s) followed the "corpuscularian" atomic model that we call the "plum pudding" model today; the particles that formed matter were spaced relatively evenly apart and evenly distributed, forming a loose "fluid", and different types of matter had different types of particles and at different densities, which gave them their properties such as weight, phase, malleability, and yes, electrical conductivity. Most people who worked with electricity thought that different types of particles carried opposing charges, and electrical current thus involved a "two-fluid transfer"; positively-charged particles moved from surplus to deficit, and same with negatively-charged particles, creating an equilibrium.
It wasn't until 1897 that J.J. Thomson, while experimenting with these "cathode ray tubes", connected the dots; using a thin cross-shaped sheet of mica placed within the tube, he showed, based on the "shadow" the cross forms on the wall of the tube, that what is passing through the tube is some sort of particle, which is being reflected by the mica. He then showed that these particles had to be negatively charged, because they were reflected by the mica sheet on the side of the negative pole, and were affected by the magnetic field of a permanent magnet as a negatively-charged particle would be, in accordance with the Biot-Savart Law and Maxwell's Equations. He reasoned that this negative charge carrier must be of lower mass than any other particle that makes up matter, otherwise some other particle would be moving to carry the charge (creating a more detectable change in mass; in fact this difference is detectable, but the ratio between charge carrier masses is over 1800:1). He named this particle the "electron" and asserted that it, and not any positive charge carrier, was most directly responsible for electromagnetism.
However, it was far too late. The convention that current flows from the positive to the negative of charged dipoles had been in common use for almost 150 years, and a lot of the work that ended up disproving it was, ironically, documented using it. Nowadays, we recognize that the movement of electrons is from the negative charge to the positive, but we diagram the movement of current in the opposite direction, as the propagation of a "positive charge", even though we now know better. That's why the positive lead or terminal is the red one, even though the source of the electrical charge is actually the negative "ground", while the actual ground in a lightning strike has a relative positive potential caused by the movement of air over it.