I believe the federal government (and notably President Jefferson) did not support the building of the Eire Canal. There were lots of other reasons New York remained larger and grew more quickly than Charleston or New Orleans. Climate, geography and free labor are some that come to mind immediately.
I'd also argue that the Erie Canal actually helped southern commerce generally and New Orleans in particular because its creation helped settle the Old Northwestern territories. These settlers then used the Mississippi river to conduct trade with the south.