Of course it’s easy to say all of this in a general way, but very difficult to experience it in the vivid and personal ways in which Catholics’ sin and failure come. In Scripture, the Church is likened to Noah’s Ark (see 1 Pet. 3:21-22). And so it has often been said, if it weren’t for the storm outside, one could scarcely stand the stench inside. “The only thing that makes the Church endurable,” the great Catholic writer Flannery O’Connor observed, “is that it is somehow the Body of Christ and that on this we are fed. It seems to be a fact that you have to suffer as much from the Church as for it but if you believe in the divinity of Christ, you have to cherish the world at the same time that you struggle to endure it.”
Why does God allow us to suffer from the Church? I think the answer is that it points us back again to the reality of the Church as the Body of Christ, where her members are saved by grace, always in need of repentance and conversion. The Church is not great because we or our leaders are great, but because God has promised us the fullness of redemption through and in her. We can often get caught up in a kind of worldly notion that the Church will always succeed in the eyes of the world. When our hopes are dashed—even in the Church—we are forced to turn yet again to God, Whose success was not in a way we would choose, but on a Cross of agony and shame. Take heart, fried, and cling to that Cross.
—from the article Life in the Ark: dealing with disappointments in the Catholic Church by David Paul Deavel in The Catholic Servant, Vol. XXI, No. VII, July, 2015