Ever seen a roadsweeper? They go along roads, sweeping up the dust and dirt in the gutters. When there aren't roadsweepers - the vehicles or the people doing the same job - cleaning the roads, dirt builds up. As buildings get demolished and sites build on with new buildings, what's underground already stays there. Over time, old surfaces get buried under new surfaces, and a bit later again, they get buried under new surfaces themselves. There's lots of stuff that make up the new surfaces. Rotten leaves, trash chucked out by people, human waste and general detritus. Where a road's paved surface is damaged and old, the old surface might not be removed or patched, but straight build up on top of. If the building is abandoned, nobody's going to be cleaning it out. Roofs or upper storeys fall in. People build on top of what's there, rather than excavating the ruins to get to the old ground level, because it's less work - and anyway, the new ground level might be higher.

If a town is abandoned, erosion of topsoil from uphill will be washed down upon it. Decomposion of fallen leaves every autumn will add dirt. Materials such as wood, thatch and mudbrick, over time will rot, disintegrate and fall in on top of items that will get preserved, like stone foundations. In the case of Pompeii and Herculaneum, literally thousands of tons of ash and mud fell or washed over the towns - huge quantities of material over a short time period.

I'd suggest taking a look at some pictures of Pripyat, which has gone without maintenance for ~40 years and is already being reclaimed by nature. Extrapolate by a few hundred years and it's not so hard to imagine how things could just get swallowed up. Dirt is blown in on the wind, perhaps some grass begins growing in the thin soil cover, the roots begin to break up the masonry, more soil blows in, etc, repeat for 400 years.

Chilari's post is also correct in that the cities you mention have been around for a very long time and generations of inhabitants probably built their dwellings overtop of older construction, so the deeper you go the older you get.

In addition to natural erosion, people often build new cities/buildings literally on top of old ones. The only History channel show I ever liked, Cities of the Underworld, was about remnants of old buildings/structures underneath modern buildings/structures.

Also- this topic is archaeological in nature (/r/Archaeology), you can look into archaeological site formation processes to find more information.