That's because those companies pay lower taxes than local companies. The real beef here isn't with the companies themselves, but with some smaller member states that steal the tax base of other bigger member states.
You are right, that's what e.g. the verdict against Ireland/Apple was about.
But this is only part of the story.
The verdict in this case was that Ireland let Apple pay lower taxes compared to other local companies.
Some other EU-countries want to tackle a different thing:
Apple (just to give an example) not paying taxes on the profit they make in each country individually but only in Ireland (in the case of Apple) for all (EU-)countries combined.