Phil Plait weighs in on the role of skeptcism, skeptics in regards to Catholic church child abuse coverup.

The one thing skeptics pride themselves on is the use of rationality and reason when making a case, yet it seems to me that quite a few are letting their emotions and prejudices get the best of them. If you perceive Catholicism as the enemy, then so be it. But when faced with overwhelming numbers against you, sometimes a head-on assault isn’t the best idea. I’m angry over this, damned angry, and heartbroken over the lives destroyed by it. But anger is a place to start, something from which we can draw energy and motivation, but we must not let it take over.

We don’t always need warriors. Sometimes we need diplomats.

My point, after all this, isn’t too hard to grasp: if the Pope did what he has been alleged to do, then he needs to be brought to justice. The Church itself looks to have been complicit in hushing up this scandal for years, decades. They too need to face criminal justice. And as skeptics, we need to be vocal about the methods employed by the Church, where those methods can be analyzed using critical thinking and the arsenal skeptics employ. But just attacking them because they are a religion is the wrong reason to do it, and attacking them with abandon, with insults, and with vitriol will not help.

It's long, but I really suggest reading Phil's whole, very well reasoned, blog post on this topic.