The major urban centers of the United States are the results of good decisions, good natural resources from surrounding lands and from topographical benefits, and good water. Most major cities in the US lie next to large bodies of water, lie along major waterways, navigable tidal waterways, or, as in the case of Chicago, around the Great Lakes. The surrounding topography favored additional benefits as these cities became major transportation hubs, first by horse driven means, then as train hubs, then major hubs for automobile and airline traffic.
As these cities lay along the major pathways that allowed the spread and migration of Americans, provided the movement of goods and people by water, and served as transportation hubs, they also were conveniently located to major agricultural and natural resource regions. From grain to cattle to stone, timber, and precious metals, the major cities were ideally suited as central drop off points for the stuff of trade and commerce.
As iron, then steel then other forms of production developed and boomed, the major cities became the ideal locations for factories, as well as for shipping the goods that were produced in the factories. The cities, themselves became meccas for people who were leaving the agrarian lifestyle, for immigrants from Asia, Europe and Latin America, as well as for American migrating populations from the East and the South, to the Middle North and the far West.
The major urban centers also became centers of culture, finance, economics, and regional hubs for governmental functions. The major wealth that developed encouraged the building of hospitals, schools, research facilities and a host of other concerns that either support commerce and life or that stand on their own as major institutions which saw a multitude of benefits to locating near or in the great cities.
The agglomeration of structured settlement that surrounds cities came from the suburbanization of American lifestyles, where light and heavy industry, along with far less congested housing and service sectors which support "bedroom communities" developed, grew and flourished, officially separated from, and far more spread out than the relatively compact land mass of the true urban settlement. In this sense, rather than abandoning the cities, people simply remained close, but not inside the limits of the major cities, where they could do a new process called "commuting" to work in the city, but living far less congested and stressful lives in suburbia.
The major cities, however, continued to grow, but upward, with the development of skyscrapers that allowed population to expand within a relatively confined land mass. And the desire of huge populations of people who wish to be fairly close to the major city, led to continuous development of contiguous, built up areas that can include cities, towns, and various areas that can go on for hundreds of miles, yet still include vast tracts of unpopulated, protected natural, and rural areas.
To this day, the major cities continue to have active ports, make active use of waterways, and serve as airline, interstate freeway, and train hubs, while maintaining growing transient working, tourist, and resident populations.