We know that there are two types of electric charges. Which one you call positive and which one you call negative is purely a convention. There are some symmetries in particle physics that tell you that there really are exactly two types of electric charges.
In contrast, there are 6 types of color charges, which are responsible for nuclear forces. They are conventionally called red, green, blue, anti-red, anti-green, and anti-blue. These are just names, though. No relation to visible colors. So there is no fundamental reason why there should be just "positive" and "negative" electric charge, at least none that we see so far, but there are exactly two.
What actually causes charge, and why it can only change by whole numbers is still unknown. Fractional charge of quarks is also a big mystery so far. They can still only change their charge by 1, but it is a flip between +2/3 and -1/3, which is a bit strange.