On the Surface, this seems to be akin to a states right issue, like we tend to have here in the US. The EU is demanding that Apple pay, when both Apple and Ireland (the country that is suppose to recive the payment) both claim that no laws were broken, nor did Apple recieve any special treatment. It would seem that the EU is attempting to generate more revenue by going a long way around and butting in to Apple's and Ireland's business deals, and eventually taxing Ireland most, if not all, of the demanded amount.
The European Commission ruled that Apple must repay the 3bn euros in back taxes that the company had claimed as tax benefits. Ireland had allowed the multi-billion dollar company to pay much less than other businesses. In effect, Apple paid just 1 percent or less. This is not fair to other businesses operating in the EU.
The EU is in place to support its members, and it is doing what it thinks is best for Ireland by ruling that Apple owes them money. One of the points of the Union is that they have more power as a group, and can pool their resources to take on big companies like Apple.
We all know why Apple is in Ireland and not in California, it's to evade taxes. On top of that, it goes and rips off the Irish government, it's like they think they are above the laws governing us mere mortals. Someone or some entity needs to hold these big tax-dodging companies accountable and the EC has done a good job of it.