Good thing this is being investigated. Tax dodging harms everyone. And of course, Apple is not the only company using imaginative tax arrangements in Ireland to minimize their tax payments.
The corporate tax rate in Ireland is 12.5%, which is quite low in comparison. If we allow a system where large companies end up paying less than their fair share, this gives them an unfair advantage (e.g. Starbucks vs. family owned coffee shop). Create a fair tax system first, then lower tax rates for everyone (if possible).
Which of course would make it useless as the tax location for the EU branches of international companies, which is at least some of their value proposition.