The fact that the details of the flights and now the prisons have had to be forced out of the government demonstrates that they did not want anyone to know about them. Not just the locations of them, which could justifiably be kept secret from the general public, but that they exist at all. This leads to the question of why the government made that decision.
Keeping these people secretly detained without official charges or any possibility of defending themselves in a court denies them rights that we would all fight to keep for ourselves. It also prevents any objective scrutiny of the conditions in which the detainees are held and the practices that they are subjected to. If we seek to condemn countries that do these things, we cannot be seen to be doing them ourselves. I believe that this contradiction provides a basic reason why these activities have been kept secret. It casts doubt on the integrity and legality of the government's actions.