Infrastructure projects like dredging harbors and rivers and mapping channels in waterways benefited the South more than the North. That may also have been true of fort construction, given that the South’s coastline was longer than the North’s.
Also, some of what Southern secessionists saw as special benefits to the North may have been designed to throw something to Easterners while the country was conquering, clearing, surveying, and populating vast tracts in the West. We were fighting wars that benefited land-hungry Westerners, and something was needed to keep Easterners onboard with that.
Also, tariffs protected industrialists in Virginia and other Southern states, as well as in Northern states, and helped to develop the industries that the Confederacy would later rely on. Additionally, tariffs benefited hemp growers in Kentucky and Tennessee and sugar planters in Louisiana. It was the cotton planters who complained, and given the controversy over slavery, their complaints gained support from other Southerners when Lincoln was elected.
At over 50% of the nation's total export, their complaints ought to carry more weight.