You don't quite have it right.
The National Deficit is the difference between the money the government raises each year in taxes, and the money it spends each year. Reducing the deficit requires increasing income or reducing spending.
The National Debt is the money that the U.S. Government has borrowed to cover each year's Deficit.
And the U.S. Treasury Bond is a physical manifestation of the National Debt. It is an IOU. You give the government money now, and they give you a Bond that promises to pay you back with interest in the future.
But you're right that the story is hate-bait. Apple, having followed all applicable laws, has money overseas. It is legally using that money to help fund the country's national deficit. In exchange for offering that credit to the United States, Apple receives an interest payment, just like any other bond purchaser. Apple is not extorting $6 per taxpayer from the Government; Apple is loaning the government its money, money the U.S. Government is not legally entitled to have, and the government is willing to borrow enough from Apple that the interest payments come out to $6 per taxpayer.
Buried in the original Bloomberg article, you'll find that Apple has to send the money back overseas when they sell the bond; if they keep it in the U.S., it becomes taxable. And the interest they make on the bond is taxable. So by doing this, Apple is helping keep the government afloat by financing the Debt, and is paying income tax on the interest they earn. They could just invest it overseas, where it would do nothing for America.
Funny how the answer isn't to eliminate the deficit and pay down the Debt so it isn't necessary to sell billions of dollars of Treasury Bonds that Apple and others can buy with foreign capital—it's to tell companies that they should pay U.S. taxes on money that wasn't earned in the U.S., hasn't been brought to the U.S., and to date won't be spent in the U.S.