Well I have watched Time Team for years so my knowledge comes from that.
In terms of buildings, it is normally just the foundations that are left from buildings and they were always underground. Any stone or bricks above ground are usually "stolen" or "robbed out" and then reused in other buidlings.
Many things found underground are related to burials so they were underground anyway.
Early man often lived in dug out pits, and of course once they were filled in what was left in the pit was underground anyway.
Also some sites were used by different people over hundreds or thousands of years, so earth was moved around to provide protection, or to make buildings, and this often buried pots and so on underground.
I think natural earth movement has also buried some things, although I remember Time Team from Turkdean where the floors of the Roman villa were found just inches under the grass after a period of 2000 years.
http://www.channel4.com/history/microsites/T/t imeteam/archive/turkdean99.html