The specific cause of each place’s burial depends on the place. Air and wind move dirt, ash, plant matter that becomes dirt, etc., around, which can accumulate over thousands of years in abandoned places.
But consider that of all the ancient places, the ones which happen to get buried, get hidden from view and disturbance by that dirt. It’s not that every ancient place got buried. It’s that the buried ones are the ones that have been preserved and kept from earlier discovery by that dirt.
So it’s not that “everything that once existed” was buried. It’s that the buried places got protected from other types of destruction and from discovery. Most places weren’t buried – but those places are already known and/or were more taken apart by people.