The thing that sets the FISA court apart from any other judge issuing warrants is that the evidence shows they act purely as a rubber stamp. Any court or judge who has never denied a warrant after having seen thousands of them is suspect.
"Never denied a warrant" is hyperbole, but the court does have a very high acceptance rate. That's a little misleading, though: the Wikipedia page mentions that the 99% acceptance rate only reflects "final" submissions, and that many requests have been changed or dropped before that point based on informal advice from a judge that the request was unlikely to be approved. Also, the NSA knows what the FISA court's rules are, and can avoid submitting requests in the first place that are unlikely to make it through. So it's not 99% of "whatever the NSA wants", it's 99% of things that the NSA thought were likely to be approved even after informal feedback from a judge. That's a very different beast.
It's valid to be concerned about the FISA court approving things it shouldn't. (In particular, I think the court overstepped its constitutional authority in approving the bulk phone metadata collection.) But the 99% approval rate doesn't support a claim that the court is a rubber stamp; it's a misleading statistic if used that way.