Why are the historical large cities in the southern US not the large cities in the South today?

I think it is also necessary to recognize that the southern states 1860 basically was in the same situation as the small states (and not so small states in Latin America) or the states in Africa after the great depression 1930:

• dependency on cotton, sugar and rice as cash crops but which is heavily exposed to changes in international commerce.
• the Northern states push for protectionism after 1800 was disadvantageous - less profits from export-focused agriculture
• the large plantations was owned by a small white minority who invested in industries in the north, railroads and luxury items - not in small scale industry (or growth of the local economy) in its neighborhood.
• the plantations was also in debt to the banks (be them in New York or London.) This, after the abolition caused a even larger pressure on the profits. This debt was large even before the civil war... ie profit wasn't as good as they could seem to be.

For example: clothing for everyone was imported from the northern states or more probably England, so also the chains necessary in the slave trade and the food for them.

The british settlers from Barbados who (according to "A History of World Societies" Wiesner-Hanks, Ebrey) colonised South and North Carolina had already on Barbados built up a number of sugar plantations. The Carolinas is very well suited to large single-crop plantations exporting rice and later cotton while the nature in the northern states isn't really suited to a system of large-scale slave worked agriculture with a cash crop as output.

One other weakness of slave labour is the capital outlay - the interests on that can pay for a fair amount of labour from free men, men which have a good reason to improve their work.

Harold D. Woodman in the journal of southern history (vol 29 nr 3) "profitability of slavery" mentions a sum of 1.2 billion dollars invested in slaves. The loss in 1865 and emancipation made that sum basically nil. One other problem which is enumerated is this: the southern stagnated and was overtaken by the North between 1800 and 1850. Why ? Was it because european emigrants didn't want to work in the South - which would have meant accepting wages only a bit larger than the planters costs for a slave.

In the same article he refers to Ulrich B Philips views of plantations as a method of organizing work and slavery as a way of exploiting labor. One of Philips points is that slaves simply in the long run costs too much - a planter had to feed and support his slaves their whole life. Slaves is also bound capital which can't be liquidated and then re-invested in some other more profitable endeavour. Because of that, slavery was for the South a one-direction road towards a road-block. Especially as the import (before 1807) and buying of new slaves required loaning capital which in the southern economy became even more scarse.

The question is still a little bit fuzzy, but I think its due to not understanding what drove trade in the pre-industrial era, so I'm just going to get into that.

The basic consideration here is transport. Prior to the invention of the railroad, shipping over water was vastly more efficient than doing it any other way. So back then it was almost more sensible to look at a country's map as its coasts and navigable rivers. Transport and communications any other way was usually so uncompetitive that it barely happened by comparison.

So to be commercially important in the 18th Century, there's one thing a city generally needed to have: access to shipping. Every major city back then was going to either be a coastal port with a good protected harbor, or lacking that at least be sitting near the end of a navigable river. The bigger the navigable watershed drained by that river, the better. New York city for example had a protected harbor on the mouth of the Hudson river, which drains pretty much all of eastern New York state, and with canal building was connected to the entire state, west to the Great Lakes, and north to Montreal.

This was considered so important that early on it was felt that every state required a port. This explains some of the odd little water-seeking panhandles in some of the early states like New Hampshire, Alabama, and Mississippi (and early colonial Pennsylvania). It is also the main reason for the east-west orientation of most Atlantic states, and the north-south orientation of Gulf states.

To go through the southern cities the question called out, Charleston is a natural harbor at the mouth of essentially all the rivers that drain the state of South Carolina (barring the Savannah basin). Richmond is near the mouth of the James, which drains all of central Virginia. Savannah is at the mouth of 2 rivers that drain the NE half of Georgia and the rest of South Carolina. New Orleans is the last (barely) viable place to put a port on the vast Mississippi, draining about a third of the US portion of the continent.

With the advent of the railroads in the 19th century, new cities begun to spring up at interior rail hubs. These include places like Kansas City, Atlanta, and Ft. Worth.

Cities with good ports of course were still important (you can't exactly build a railroad over the Atlantic), but you only need so many of those, so port traffic had a tendency to become consolidated to the larger better-equipped ones like New York, New Orleans, Chicago, and Norfolk etc. Cities on rivers (without ports) were still important, but railways were now where the growth was, and those don't require a river. So while Richmond still grew, its growth was nothing like Atlanta's.