I don't consider the NYT a reliable source on this issue after their machine translation flub that apparently turned something like "should be strongly censured" into "should be strictly secret". Using Yahoo!Translate on a "smoking gun" memo is pathetic and strongly suggests that they're looking for any stick to beat the RCC with.
I agree on Sean Brady since he seems to be self-incriminating.
In response to blaming Ratzinger for not defrocking someone while not being Pope (??) I keep seeing pieces like this:
The Vatican looks secretive and the media looks agenda-driven. I've been trying sites like GetReligion meanwhile. But every side keeps contradicting the other and they constantly seem to have a legitimate basis for saying "you left out so-and-so which is relevant to the case..."
Regarding the NYT and the catholic church, i could easily point out one mistake the catholic church made in it's history and claim the rest invalid based on nothing but it, but it is not a valid technique so i will refrain from it.
The NYT article is about a bishop who has moved a molester around instead of turning him in to authorities. Are you denying such things happened? Then you really have had your head in the sand on such issues. Or you are using the NYT as an excuse to not have to think about it. But to humor you, here's: 1 2 3 4 5 quick examples. If you want more, google will be more than happy to help you.
Cardinal brady is certainly not alone either.
In the arizona case with Ratzinger, the priest has said that he knew he was to be defrocked, and did not appeal. Even if he did, It is not up to the priest, the bishop, the cardinal, Ratzinger, JPII, or jesus humself to decide whether the case had merit. It is up to the judicial system, and every single person in on the secret trial is guilty of covering it up simply by investigating in lieu of, instead if in addition to, the local authorities. Plus in that case, the priests behavior was described by his own bishop as 'satanic'. But no rush, a 12 year trial is perfectly reasonable.

Oh, maybe the press would "get" religion more and leave out less relevant details if the catholic church hadn't gone to (and CONTINUES to go through) truly superhuman efforts to keep every last detail a secret!
edit -- oh, i forgot one more group we can blame -- the archbishops!