Agreed, and as important, political power in the South & Washington DC lay in the hands of slave-holding planters who had little interest in promoting Southern shipping and did not defend it in Congress.
So, where DiogenesLamp blames, in effect, Yankee devils who "wrecked the Southern shipping industry", in fact Southern shipping was not defended vigorously by those Southerners who had the political power to do so.
I also suspect steamships played a huge role since they required an extensive manufacturing base -- much greater than wooden sailing ships -- which again Southern planters had little interest in developing in the South.
New Yorkers established steamship routes to Charleston, New Orleans, and Galveston early on. They also had extensive trade with Mexico, the Caribbean, Latin America, and eventually, California. There was a lot of shipping going on that had nothing to do with cotton, and it takes time and effort to uproot or kill off such established trade connections, and the advantages that a widespread trading network brings.
As concerns the Midwest, the refrigerated railroad car was coming. The earliest models were developed in the 1860s and by the 1880s they were common. This encouraged trade between the Western plains, the Chicago slaughterhouses, and the East Coast urban masses. Of course people didn't know that in 1860s, but the provision of food from the West to people in the East would do a lot to tie the North together. The South wasn't very involved in this, and the decline in cotton prices at the time would keep the South out of the loop.