Anyone who has lived in a drafty old house or apartment knows what happens to warm and cold air inside when there's too little insulation and too many cracks and gaps: The air escapes, resulting in wasted energy. Improving energy efficiency is a big part of green building stewardship, but having a tightly insulated building envelope can prevent or impede proper air flow inside.
Homes with natural air ventilation systems have windows, of course, so people can regulate the air. But if the homes remain closed up, the insulation often is so efficient that clean, new air from the outside doesn't come in on its own, which can lead to unhealthy, stale air inside. Furnishings made with chemicals and allergens from pets are just two aggravating factors when air is stagnant.
Residential code regulations are a bit behind the commercial ones, but where green codes have yet to fill the gaps in codifying what to do, informed builders and designers will self-regulate for safety. Having mechanical exhaust systems, particularly in areas with long hot or cold seasons and lots of time with windows closed, is essential for healthy indoor air.