Peter Galbavy,
Well the Irish government decided on a policy of a friendly business environment and low corporation tax rate in order to attract multi-national HQs to boost their economy. And it's broadly done well for their economy. So of course they're going to object to having this affected by the European Commission. They've got to keep looking like a friendly place to base your HQ - otherwise there's always Luxembourg, the Netherlands, Malta etc.
On the other hand, it looks like they did give Apple a special deal, that other multi-nationals didn't get - so you could argue there's no threat to that economic model from this. But I think they've decided it pays to make sure companies know they're maintaining that policy.
I'm sure they can think of lots of nice things to do with €14bn.