Read the history of the Commerce Clause. The all-encompassing definition of the clause is fairly recent, mainly established by FDR's New Deal.
Well yeah, since the clause wasn't really used by the federal government until the 1900's, as your link emphasizes. It's illogical to assume that since the commerce clause wasn't used in the past to prohibit commerce among the several states, that meant the power to do so wasn't there.
I would like to see something that says the Commerce Clause was limited to ensuring a free trade zone between the states.