1) Plants trap carbon. When they die, they gradually build up the ground beneath them. This is why "dirt" is deeper in areas with plentiful flora than deserts.

2) Buildings are natural windbreaks. They stop windblown dust, which builds up around them.

3) Prior to germ theory, moving waste outside cities was rare and reserved only for truly noxious waste like corpses. Everything else was effectively dumped next to the structure, slowly raising the ground level.

4) Digging up foundations was monumentally difficult, particular prior to building codes and hydraulic machinery. Ergo plowing over old buildings was a heck of a lot easier than digging them up and starting over. Multiple by a couple thousand years and presto, your city is now a tel.

5) Prior to harnessing electricity, light and heat were dependent upon fire. This created a perpetual fire risk which tended to burn down some or all of a city pretty regularly. Rebuilding ubiquitously occured a top the ashes.

Sands shift over time and water can move an immense amount of soil over a few millennia. Furthermore any cities remaining above ground are almost immediately cannibalized and destroyed to build new ones so many of the ones newly discovered are going to have been hidden so they avoided this fate.

I really don't know, but I think if I said "jews" I wouldn't be wrong.