The directive that is now codified as 2009/24/EC was a direct response to the German Federal Court’s (BGH) decision nicknamed “Inkasso-Programm”, where it ruled that a software needs to reach the level of creativity usually required for any kind of work to be protected by German copyright law (“Schöpfungshöhe”). According to the Court, programs only rarely cross that creativity level and are thus public domain usually, unless unusually creative. The Member States and the Commission found this unsatisfying naturally, especially with the USA already protecting programs with their completely different copyright system. As a result, the mentioned directive was issued whose primary purpose was to lower the creativity burden without ditching it completely. Germany implemented it later in §§ 69a ff. UrhG, so that programs now usually fall under copyright.
When the copyleft effect of the GPL kicks in is highly debated, which the article does not really mention. There is no consent about this in jurisprudence, and GPL cases are surprisingly rarely taken to courts to clarify this particular issue. The ongoing case against VMWare might give some opportunity for courts to clarify, but it is not over yet, and I suspect it will not cover all possible aspects. The case of dynamically linking a GPL'ed library is an especially hot topic.
There is an ongoing debate as to whether copyright law is the correct place for software protection at all, because in Continental Europe, the concept of copyright is mainly focused on the author’s personal creativity and only sees the commercial use of works as a necessicity for the author to make his life. The concept of copyright cannot be thought without the author, who is connected to his work for all of his lifetime. If it weren’t for several international treaties mainly drafted by the USA, software protection law in Europe would probably have taken a very different way.