A. The mass of the atom is too small and difficult to operate, so it is not the content of the atom, so A is wrong.
B. The mass of the molecule is also very small and difficult to operate, so B is wrong.
C. The proton has a very small mass in the atom. It is difficult to measure its mass in practice, so C is wrong.
D. Elements are macroscopic concepts that can be measured using instruments, so D is correct.
So choose D.