I am not referring to intentional burials by a people existing at the time of an artifact or even by people attempting to conceal a site or artifact. I am referring to the fact that many locations and items seem to simply become buried under layers of earth whether three thousand years old or three hundred. This seems true even in locations which are not known for excessive seismic activity nor floods or mudslides where this phenomenon would have a natural conclusion.
For example, many Roman structures in the UK and other parts of Europe have been unearthed but were completely underground even when they are five meters tall or bigger. In London, I know many buildings were simply “built over,” but how are other sites simply “going underground?”
What you are describing is a process called 'site formation' in archaeology - you can read up on it in much more detail in any of the standard introductions, of which the main one is Colin Renfrew and Paul Bahn, 'Archaeology - Theories, Methods and Practices' - I think the most recent edition was the fifth in about 2015.
There are really three answers to your question, depending on what the site is made of and where it is:
(The least common) - sometimes the environment changes, naturally or artificially burying the site. The most famous example would be Pompeii, but most such sites are on the coast, where sea level changes or coastline shifts bury them, or near rivers - sometimes, as with the building of the Aswan Dam in Egypt, shifted by human activity. This is the only situation in which the full-size walls that you describe tend to be found mostly intact, except when a building has been deliberately preserved.
Buildings made of stone are usually dismantled by people looking to reuse that stone - such repurposed bits of masonry are called 'spolia'. This goes on until only or little more than the foundations - dug into the ground and so difficult to remove - are left at ground level. At this point, vegetation can grow over them and begin dying and decomposing to form soil - although plants will not grow as tall over stone foundations, leaving marks in the field (cropmarks) which can be picked up in aerial photographs.
Most buildings throughout time have not been made of brick or stone, but of perishable materials (usually mud-brick or wood) on top of stone foundations. In these cases, the perishable material rots away, forming fertile soil on which crops grow and obscure the building, which is then doubly buried - first by being reduced to its (buried) foundations, then by causing it to be covered by soil and plants.
Essentially, the idea that archaeologists find high walls all over the place is not quite right - under normal circumstances, what is left is just the foundations. The exceptional cases make the news and attract so much interest precisely because they are exceptional.