The primary reason is that soil accumulates over time. Erosion tends to move soil from higher elevations down to the lowlands where humans inhabit, increasing soil depth and burying ground level structures. This is particularly extreme on floodplains and river valleys, where soil builds up relatively quickly. Waste and human detritus also tend to accumulate around structures due to human activities and wind, further burying structures.
There's also a degree of selection bias though. Structures that aren't buried rarely survive long enough for us to excavate them today. They get bulldozed over or eroded away by the elements. There's an excellent example of this in the Gila River valley of Arizona, where two major sites were constructed and occupied contemporaneously. One of them, Casa Grande had preservation efforts taken in the late 19th century. Casa Grande had a nearby sister site named Casa Blanca where no preservation was attempted. The aboveground ruins of Casa Blanca have entirely disappeared in the century since those reports due to erosion from rainfall...... just write the main parts!
