The title itself speaks a thousand words. The article itself isn't quite so long, but it has lots of interest factoids in it.
First, there really isn't a central agency, in any country, that tracks and monitors all space assets, near or far. The U.S. has a pretty good system going, but not every country, especially those not-so-friendly with us, report all space launches and destinations. And even if they did, the initial trajectory on which a spacecraft is set isn't necessarily it's final trajectory.
I'm personally in the business of sending spacecraft to other planets, and recognize that doing planetary fly-bys are par for the course. We do it all the time as it is a cheap and easy means of gaining or draining energy from a spacecraft's orbit. We spend an enormous amount of time and money to ensure that a fly-by doesn't accidentally become an impact.
Yet whenever the public gets word that we're doing a fly-by of Earth, people start to panic -- especially if there's a nuclear power source on board. For example, when the good ship Cassini flew by Earth several years ago, the doomsayers were out in abundance. Here is one such example. In the case cited in the title article of this post, Rosetta certainly isn't the Battlestar Galactica (neither was Cassini), yet people start to believe these things are going to land on their heads. Because of this, most of the time it isn't widely published as a "Big Deal" that a fly-by is designed into a spacecraft's trajectory.
This has both good and bad things about it -- it allows a space agency to proceed without dealing with a potential and usually totally misplaced public uproar (which is costly -- especially if it ends up in courts), but it has the stench of "cover up" if such an uproar does end up occurring (which is also costly -- to do public damage control).
Nevertheless, planetary fly-bys are good. One of the finest examples of these is the "Grand Tour" performed by the Voyager 2 spacecraft as it flew by Jupiter, Saturn, Uranus, and Neptune on it's way out of the solar system (see the image, below). Each fly-by allowed it to pick up speed to get to it's next destination. Even Galileo used fly-bys -- of the inner planets, no less -- to get to Jupiter, and then used them all the time to guide it's trajectory around Jupiter and it's moons (the Jovian system).
Still, the article cracks me up. People were right on the verge of panicking, but a moment's hesitation saved a lot of people a lot of embarrassment. I wish it were always so in my business.