Charge isn't really made out of anything so to speak, its just an intrinsic property of matter. It can be described, but that's really about it. Protons have a positive (1+) charge because they are made up of two quarks with +2/3 charge and another with -1/3 charge. Electrons just have a negative charge, because well that is just the way they are. Also you don't necessarily need to have opposite charges neutralising each other. In things like atoms however it is more "stable" to have a neutral charge overall.
Observationally, I would just say that certain particles exhibit an electrostatic repulsion with the same type of particles, so that brings in the concept of charge. Then we also find that these particles can exhibit electrostatic repulsion to certain different types of particles, and that brings in the concept of sign of charge. The only other connection between protons and electrons is simply that they are both extremely common. Then the reason we tend to find them together, and in cancelling numbers, is that if we did not, there would be huge electrostatic forces that would act to change the situation until they did cancel.
Or maybe you are asking why is there roughly the same number of protons and electrons in the universe as a whole, and that's actually a pretty good question-- I have no idea, and maybe that is as difficult a question to answer as why is there more matter than antimatter. Note that if there were equal amounts of matter and antimatter (so annihilation didn't prevent that), then the electrons would just draw in equal numbers of positrons and you wouldn't need a similar number of protons to achieve charge neutrality.