One point that is so basic that physicists often forget to explain it: leptons and quarks don't really have a "size," they are considered point particles. A proton is a configuration of three point particles though whether it makes sense to say that this configuration has some spatial structure is beyond me.
Also, mass has nothing to do with size, or "stuff"-ness. A proton has about 100 times more mass than its quarks (from binding energy), but an atom has less mass than its protons and electrons added up (from the loss of potential energy). A top quark has about as much mass as an atom of gold, but again is just a point particle. And photons have no mass but the energy of photons bouncing around in a confined space does have mass.
Also, mass has nothing to do with size, or "stuff"-ness. A proton has about 100 times more mass than its quarks (from binding energy), but an atom has less mass than its protons and electrons added up (from the loss of potential energy). A top quark has about as much mass as an atom of gold, but again is just a point particle. And photons have no mass but the energy of photons bouncing around in a confined space does have mass.