If a country, say Ireland in this instance, wants to attract a large corporation to create jobs and revenues, long term, in their jurisdiction then they should have the power and ability to offer whatever incentives that they feel give them the competitive edge over other jurisdictions.
IMHO, that's why the EU is wanting to fine Apple and Ireland - to punish Ireland for doing what was on the best interest of Ireland.
We do the same thing here in the US, in that the individual states have the power to create whatever incentives they feel would attract businesses to open in their jurisdiction to create jobs and revenue for the state, including special tax rates, land deals, public money used as financing for the company, and many other incentives.
I see nothing, as far as what's been discussed here, that justifies being upset with Apple or Ireland. Maybe that's because I'm neither a Progressive, or Socialist, or believe in false and forced equality of outcome schemes like those the EU seems to love.
It's been stated already in this thread, but at the risk of repeating others, this is a perfect example of why the UK probably made the right choice with Brexit.