This article is too hysterical and exaggerated without a single concrete example. 

Journalists are seriously persecuted in undemocratic countries, but that's always been the case. There are plenty of examples to cite.

But in countries that guarantee press freedom, what can  governments do against journalists they don't like?

One recent example was Donald Trump excluding the New York Times from his press conferences. But that's not a serious persecution; the Times merely has to send a freelance to cover the conferences for them.