It is a complete and total historical accident. As early as the 18th century, long before the discovery of the electron or any other subatomic particle, it was known that there were two types of charge, and that like repelled and unlike attracted. The choice of which we would call negative and which we would call positive was completely arbitrary.
Many years later the electron was discovered, and it turned out that it had the kind of charge that we had been calling negative: https://xkcd.com/567/