The letter they posted is signed Tim Cook, and does indeed refuse the EU's claims, however it contains obvious lies of omission and seems to demonstrate a complete lack of understanding of how the EU works.
The Commissionâ(TM)s move is unprecedented and it has serious, wide-reaching implications. It is effectively proposing to replace Irish tax laws with a view of what the Commission thinks the law should have been.
No Tim, the EU member states have all agreed on some basic ground rules for taxation so that they can have a free market without any of them gaining a competitive advantage. It's hardly a shock to anyone that the extremely advantageous tax arrangements in Ireland were incompatible and the EU has been warning Ireland of this for many years. In fact Ireland changed its laws in 2010 to block companies from doing what Apple did, and as I'm sure you are aware even Apple will have to find a new corporate structure by 2020 or start paying that tax anyway.
The letter is pathetic. It makes out that Apple did Ireland a massive favour by opening a factory and bringing jobs, ignoring that it only did so in order to dodge billions of Euros worth of tax that rightfully belonged to the Irish people.