The problem is his tendency to equivocate. The priests did this, therefore, the Catholic Church is bad. The Catholic Church is Christian, which therefore makes Christianity bad. Christianity believes in God which makes God bad. People that believe in God are therefore bad.
As with many crimes in our society, the cover-up is usually more damning than the actual crime. In this case we see the church applying pressure to its followers using religious authority. We see religious belief clouding peoples judgements.
As an atheist I am more than willing to say that religious people are just as flawed as atheists. I don't view christianity as bad because there are christians who are pedophiles. What I view as bad is the use of threats/pressure from higher ups under the guise of religion. Something to the effect of, "You will ruin the church if you reveal these secrets, and God might not look kindly on this." Or, "If you make the church look bad just imagine all of those souls that will be lost."