This is ONLY about retroactively changing the agreement in order to collect more money. Apple's had offices in Ireland since 1980 and hoards of cash there for decades. Why wasn't this disputed during all that time? Oh, that's right, now that Apple's the biggest company in the world the EU suddenly want their money by conveniently claiming it's illegal. Can't wait until Apple pulls out of there, cash, products and all. Losing EU sales would be like losing sales in one US state anyway.
No, I suspect laws and regulations have changed and Apples relationship to Ireland has changed, and if you are going to attempt to try and make this out as picking on Apple because they are big or rich? You really have no idea about how the EU courts and bodies work and what they have and are doing. Google and Amazon and as mentioned in this story Starbucks haven't escaped.
Giant corporations not paying taxes is also a VERY public issue across Europe and so another reason action has been taken.
If Apple pulled out of Europe I would guess their profits would drop by a third or so, good luck with that idea.