The cotton tax was one cent per pound, not 1%. It was a war tax that went into effect in October, 1862.
Do you seriously contend it was a contributing factor to southern states seceding in late 1860 and early 1861?
http://www.jstor.org/stable/25106505
Right I meant to correct that 1 cent not 1%.
Morrill Tariff was a large contributor to Southern issues with FedGov.
Only $3 million was collected(I guess in border states) prior to the end of the war from cotton taxes. Not that significant.