I'm reposting a comment I originally made over at Beggars All in response to a Catholic disputant:
“The double standard requires that we only focus on the short comings of the perverse members of the Catholic Church who violate her teachings...and to further the violence towards intellectual honesty, we are also required to fallaciously attribute such immoralities to the entire Church via hasty generalizations and faulty moral reasoning despite said Church's opposition to those very immoralities.”
Except that Alex is comparing the incomparable. In Protestant theology, Protestant doctrine is separable from the Protestant organizations (e.g. denominations, seminaries, colleges) which institutionalize its doctrine. If, say, a Protestant institution were corrupted, that wouldn’t logically reflect on Protestant theology inasmuch as there was never a one-to-one correspondence in Protestant theology between our doctrines and the particular organizations which institutionalize our doctrines. Protestant institutions come and go. The theological tradition is portable.
By contrast, Catholic theological tradition is inseparable from its institutional identity. The “one true church.” Hence, everything sticks to the Roman church.
If the Roman Church has policies which promote various forms of abuse, then that indicts the institutional church. Likewise, if the Roman Church, in the face of abuse, engages in a cover-up, then that also indicts the institutional church.