In F. Wilczeks book, The Lightness of Being he describes his theory on the origin of mass. He explains, in much more detail, about how color charge carried by quarks disturbs gluon fields which increase with the distance from the quark. Then he explains that this energy cost is nullified by an antiquark of the opposite charge nearby. This doesn't cancel it completely because of some [pesky!] rules of quantum mechanics. He says, basically, that there is some residual energy left over after this "canceling-out" and using the equation m=E/c2, we find the mass of a proton. I'm sure I missed something; all I see he did was explain where some excess energy has come from, when/where does that energy become mass? I hope I explained everything clearly enough to make sense!