Yet on Sunday, the archbishop sounded upbeat.
Dolan said nothing in his homily about the pedophilia scandal, but he later defended Pope Benedict amid charges he did nothing as a Cardinal years ago to punish a Wisconsin priest who abused more than 200 deaf boys.
"We Bishops for a long time have been saying we could have handled things a lot better," Dolan said. "We've been for a long time owning up to this, expressing contrition, regret, a desire to do better."
But outside St. Patrick's, a handful of mostly gay men protested, accusing the church of not doing enough about the child abuse scandal.
"No one is holding them accountable," protester Todd Fernandez said. "How many of them have gone to jail?"
"As a gay man and a Catholic, I'm tired of taking the blame for what these pedophiles are doing," protester Rich Murray said.
Last week, controversy flared when the pope's personal priest compared attacks on the pope to the suffering of the Jews.
Even a Vatican spokesman disavowed such a comparison.
But many Catholics seemed exhausted Sunday of a scandal that just keeps going.
"This happened many years back," Catholic Helen Moreno said. "I mean, give it a rest."
"I think there's nothing perfect," Catholic David Argento said. "And just so long as we know the Catholic Church is addressing it and taking the appropriate measures."
As for the archbishop, he said he didn't pay attention to much of last week's controversy. He said he was busy preparing for Easter. Dolan seemed anxious to move on.
"I'm wondering if we've said too much and wondering if the best thing to do is say thanks be to God for the hope that passover and Easter bring to all of us," he said.
Dolan was asked about how he recently compared the suffering of Christ to the difficulties facing Pope Benedict. He said he stands by his remarks.