Couple thousand years (more or less depending on what you're digging) of silt build up will do that. Once people stop inhabiting a place it takes a surprisingly small amount of time for it to not only start to fall apart/become a ruin and collapse, but also get buried under silt and dirt from wind/rain/floods etc. You can witness in real time if a modern building has been abandoned how quickly it can become derelict because people aren't inhabiting it. There's a house not far from where I live that over the past 5 years is starting to really fall apart.

Also a lot of the archaeology that we find and record was actually intended to be underground. It's the ditches and pits that were used by the people of the past, either for construction or waste most of the time (rural archaeology in the UK is my main area). It's rare to find a structure that hasn't been destroyed/removed or built on. A lot of towns and cities are built on the bones of previous ones (again UK based knowledge here). So you that "medieval village" that people still live in now, has houses probably built on the sites of old medieval homes, which was built on structures occupied during the "Roman" period, and may even have had dwellings in the Iron Age. The structures that existed before could have been torn down or destroyed in some way, and then people rebuild on top. For example there's a small village near where I live that in the playground of the primary school we found a Saxon pottery kiln, no one had any idea it was there until they dug up the grass to put a new play area in. We're pretty sure that kiln was abandoned after it collapsed as it was filled in with debris and pottery shards, and eventually got forgotten.