It's usually used in place of a person/active participant in something.

So ‘Brussels suffered a deadly fire’ will always refer to the city. ‘Brussels decides on new aircraft regulations’ will almost always refer to either the city government, the Belgian government, or the EU Parliament headquartered there. Brussels is just an exceptional case because there is so much based there, as opposed to the Hague or the Vatican.

They might say "The city of Brussels".