Exactly. The EU's beef is primarily with Ireland, only secondarily with Apple. The thing is: Ireland is a net receiver of EU money. So the EU reasons: if you want subsidies, you have a certain obligation to pick up certain types of money, taxes being one of them. Otherwise it would create a perverse incentive to EU nations: don't collect taxes, let the rest of the EU countries pick up the bill. So the EU demands, in exchange for membership, a tax regime of a certain quality. Since they are the ones paying, they decide. Germany, for example, could decide not to tax Apple a penny, but it wouldn't get a similar frown from the EU, since it's a net payer into the system.
So the EU says to Ireland: collect, or we'll lower your subsidy by an equal amount. And Ireland finds itself caught between a rock and a hard place.