The Washington Post has the story here. In particular, the judges are upset by the suggestion that they are collaborators rather than independent arbiters of Executive Branch requests for orders to amass vast amounts of e-mail data from American citizens. They should be upset, but they shouldn't be surprised. One of the disadvantages of a secret court is the likelihood that its work will be inaccurately characterized by journalists and others, who are deprived of access to information about its actual operations.
What should upset the federal judges more than allegations than that they are hand-in-glove with the Executive Branch is the fact that they are operating a secret court, like England's Star Chamber, which was abolished in 1641. The standard justification of a secret court is to avoid tipping off potential subjects of investigations, including would-be terrorists. I've never seen an argument, however, as to why secrecy would be more effective (let alone more legitimate) than making sure that potential terrorists know that they are being closely watched. True, they might stop using e-mail and telephones as methods of communication, but wouldn't that, in itself, disrupt their planning efforts? After all, if they are forced to resort to carrier pigeons or hand-carried messages to conspire, would that itself seriously erode their capabilities?
So, to all the politicians (including the POTUS) who are adamant about the importance of secrecy in the process of tracking terrorists, I pose a simple question: Why are you so sure that complete secrecy is preferable to loudly publicizing (or even exaggerating) our technological ability to intercept the communications and disrupt the activities of terrorist organizations? Please explain your reasons to us. Don't simply insist that secrecy is necessary and that the program has disrupted several planned terrorist attacks. We already know that you prefer keeping secrets from the electorate just because you can. But that is not a reason to do so.
By the way, throughout this post I have accepted as given that the NSA's secret information collection is entirely about protecting the US from terrorist threats. But if that's the case, why has the NSA allegedly been bugging EU offices in the US and engaging in cyber-attacks against EU organizations (see here)? And, assuming the allegations are true, were those activities approved by the completely "independent" federal judges serving on our government's secret court?