Historically cities were liberalizing (as compared to the feudal countryside) - see the free cities of medieval Europe

Cities are also sites of manufacturing, craftsmanship, trade and cooperation.

Do your criticisms apply to Singapore, Hong Kong and Tokyo? Do they apply to Monaco, Florence, and Barcelona? Both at present and historically..?

Perhaps your criticisms are more of modern nation-state socialism than cities.

The idea that people are packed together is at least partly the result of zoning regulations that allow ultra-dense housing or single-family homes, with little in between. In contrast organically developed cities show a continual rebuilding that has resulted in a gradual transition from the dense areas to the outlying areas, with many middle forms of housing in between.

Another aspect you seem to be taking for granted is modern policing. New York City did not have a police force until 1845, surviving for over two centuries on the back of armed citizens (who maintained daily order) & marshalls and sherrifs (as agents of the courts enforcing specific orders). This was the historical pattern throughout the European world, including England.