Basically, what are the geographical, political, social, and economic reasons for a city to form when and where it does?
There are several important factors, and large cities in the post-industrial world have usually benefited from more than one:
Strategic location Defending access to a navigable river or important mountain pass for military or nationalistic reasons.
Good harbor Protected from storms, with deep anchorages adjacent to solid, dry land at nearly the same level as the water. Can also apply to the head of navigation on a large river, though that also usually corresponds with . . .
Source of power At the fall line of a river, which offers good water power, or near coal deposits.
Transportation breakpoint A place where goods on big ships must be transferred to smaller vessels or to railroads. Since the goods are being unloaded and reloaded anyway, it's a good place to set up a factory to add value to those raw materials or partly finished products.
Seat of government National or state capital, or the site of a royal court.
Focus of specialized knowledge A place where new industrial processes arise, where the inventors and specialists cross-pollinate new suppliers or producers. Think New England mills, Michigan-Ohio-Indiana automobiles, Bay Area semiconductors and software, Southern California aviation.
Distinct regional capital For wholesale and retail trade, natural "territories" coalesce around a primary city. This is self-reinforcing, and that city grows simply because it already has the gravitational attraction. Banking and business adminstration services then follow the same lines. Dallas and Atlanta are good examples.