So, authorities in the European Union knew about this practice. Well, there's a surprise. NOT! I'm sure the biggest issue in the EU with regards to this practice is that the US authorities can't do enough to keep such things out of the press.
Transporting people on "secret flights" is one thing, but torture is another. The two issues have been, wisely, fused by those in the anti-war camp. I have no problem with al Qaeda members being whisked off for long stays in Guantanamo or wherever. They are, after all, the enemy. Torturing them is another issue.