It's a little bit tricky with the protons, as free quarks don't exist. One could argue that the mass of free quarks is infinite, which explains hadronization: i

It's a little bit tricky with the protons, as free quarks don't exist. One could argue that the mass of free quarks is infinite, which explains hadronization: it is energetically cheaper to produce quarks out of nothing so that the quarks are not free. What is certainly true is that, writing down the QCD Lagrangian, there is nothing which tells you the scale of the proton mass, nor the somewhat different scale of the pion mass. This is in sharp contrast to the Hydrogen case, where the masses which appear in the Lagrangian are very close to the total mass of the Hydrogen.