The molecules in a bar magnet have electronic orbitals that are aligned in a certain way, and kept in orientation by the pattern in which the molecules arrange themselves in the solid state. The moving electrons create the magnetic field.
With iron, my understanding is that each atom has a reasonably strong magnetic field, but there's nothing forcing them to align, and as such, random vibrations associated with temperature cause the individual fields to be constantly changing direction. Only when an outside magnetic field is imposed do the atomic fields line up, which enables iron to "transmit" magnetism that's applied to it.
Your analogy to the atmosphere makes a certain amount of sense, but it still leaves me with the question of what prevents the charges from rebalancing. The atmosphere is a very poor conductor of electricity, so it's easy to see how imbalances of charge can build up. But in a metallic core, I would think that imbalances should dissipate before they even build up. But of course, I'm far from being an expert in all of this.