Sure it is because apple got the illegal state aid and should not have gotten that, it has to pay that now.
You're obviously reading something in this that I am not. How is Apple following Irelands tax guidelines illegal? If it was illegal for Ireland to present them, then why has it taken over a decade for the EU to do anything? Could it be that the EU is - like many large governments - a corrupt place that didn't act until pressed by the U.S. Congress to do so?
Their system is broken, and demonizing Apple isn't going to fix it.