As another poster earlier stated, the government is doing me no favor by only confiscating 50% of my money, and saying I should be happy I get to keep the other half. (to be further taxed by other government agencies)
It makes some sense for a government to tax businesses within its borders because the state government is allegedly providing services for that business. That state is providing no such service for businesses in other states. If you read through the "Federalist Papers" and "Letters from a Federal Farmer" you'll find several in depth discussions of repercussions of having taxing power of entities in one state from another.
Overall, it wasn't considered beneficial to the nation, as the experince with the Articles of Confederation showed.
I believe another poster here pointed you directly to the relevant Supreme Court decision on the matter, which discusses the facts (and probably history of) all this. I haven't had time to read through it, but may try to squeeze it into my schedule soon, as it sounds interesting. Do you have any comments about the particulars of the ruling, (which generally held against your proposition)?