A, the mass of the atom is too small to operate, so it is not the content of the atom, so A is wrong.

B, the molecular weight is also very small, which is not easy to operate, so B is wrong.

C, the proton in the atom has a very small mass, so it is difficult to determine its mass in practice, so C is wrong.

D. Elements are macroscopic concepts and can be determined by instruments, so D is correct.

So choose D.