If you break it down to the smallest piece, you're talking about Carbon atoms with an atomic mass of roughly 12 versus (mostly) Nitrogen and Oxygen with approxi

If you break it down to the smallest piece, you're talking about Carbon atoms with an atomic mass of roughly 12 versus (mostly) Nitrogen and Oxygen with approximate masses of 14 and 16. So it's lighter as atoms but not by six times. Most of the Oxygen in our atmosphere is O2, so there's a bond and space between the atoms as well as space between the molecules and others. In the same way, perhaps the carbon is more like closed cell foam that has voids that exclude other atoms. These voids have no mass but contribute to the effective volume.