This is actually a fairly misleading article. The Germans are voting in Pirate Party candidates in the state parliaments in very small numbers; there is simply no way they are going to become powerful enough to "take over" the state parliament in any of the larger German states. They join other fringe parties in having a seat at the table, but it is chiefly a country run by people who enjoy much larger margins of victory in the elections that are being held, leading to the Federal elections.
The Pirate Party is chaotic and disorganized, and the Germans don't do chaotic or disorganized. They do value privacy, and that's an issue where the Pirate Party does well. But they simply don't do well enough to make much of a difference.
Now, do these things build and snowball into larger victories? Absolutely. But the issues that the Pirate Party run on aren't mainstream enough to create those victories in the state elections.
The Green Party, for example, won in Baden-Württemberg by running on the nuclear power issue right after the Japanese tsunami disaster; this has meant that the Greens are shutting down nuclear power. The Pirate Party isn't running on anything that significant for the average German. They're worried about having the right to steal intellectual property and, well, that's just not a winner in a country that manufactures products based on the right to hold and maintain intellectual property.
When it dawns on people that the Pirate Party wants to make it legal to steal information, the Germans who make things will realize that the Pirate Party is going to try to put them out of business. That's because it wants to make the Internet an uncensored free for all; this would make it legal to post the plans for a certain car or electronic device online so that someone in another country can copy it and make it cheaper. That, in turn, is not going to lead to many votes.