Lets use hydrogen as an example, hydrogens molar mass is ~1g, this is to say, that 6.02*10^23 hydrogen atoms have a mass of 1g, the molecular mass of a Hydrogen atom is ~1/6.02*10^23 = ~1.66*10^-24, this mass doesn't encooperate electrons or isotopes in my case, cooincidently, this mass is also equal too the mass of one proton, the mass of a proton is equal too the mass of a neutron, the value 1.66*10^-24 is roughly equivalent to 1u, an atomic mass unit.
Now as for any element appearing to match up to the number of protons/neutrons in it, this is because a mole is a humanly derived quantity, a mole is 6.02*10^23 atoms, we use it for sake of ease, it is defined as the amount of substance that contains as many elementry entities as there are atoms in 12g of carbon-12.
Carbon-12 has 12 elementry particles (6Protons 6Neutrons), 1g of the 12g that Carbon-12 is made of is equivalent to the molar mass of a neutron or proton, which is why they "match up", everytime you go up 1g in molar mass, your effectively adding 1mole of protons or neutrons.
If you divide this extra mole of protons or neutrons by avagadros constant, you end up with a singular unit of the proton or neutron, so for an example, dividing carbon-12's molar mass (12g) by 6.02*10^23, your effectively finding out the molecular mass of 6 protons and 6 neutrons, much like if you divided the mass of 1g of Hydrogen, your finding the molecular mass of 1 Proton because hydrogen contains 1 Proton, and 1 mole of Hydrogen is 6.02*10^23 protons.
The molecule is created by the laws of physics, moles are a quantity of molecules created by man in order to make calculations easier, because if we went around stating everything in terms of the amount of molecules it contained, rather then moles, or kilograms, we would be stating massive numbers.
EDIT: A better way of putting it is that a mole is the "Gram weight" of a molecule, so if a molecule weights 12u, then its molar mass is 12g, which is 6.02*10^23*12u molecules