Their corporate headquarter is in Ireland. They pay payroll taxes, VAT etc. in each EU member state just like every business has to. They do not, however, have to pay taxes on their corporate earnings in EU countries other than Ireland. That is a central part of "Freedom of Commerce" in the EU. (One of the EU's 4 foundational freedoms.) What Apple has been rightfully accused of is not paying their taxes on corporate earnings in Ireland.