"Listen. What's the routine on joining a monastery?" I asked him. I was sort of toying with the idea of joining one. "Do you have to be a Catholic and all?"
"Certainly you have to be a Catholic. You bastard, did you wake me just to ask me a dumb questions"
"Aah, go back to sleep. I'm not gonna join one anyway. The kind of luck I have, I'd probably join one with all the wrong kind of monks in it. All stupid bastards. Or just bastards."
When I said that, old Ackley sat way the hell up in bed.
"Listen," he said, "I don't care what you say about me or anything, but if you start making cracks about my goddam religion, for Chrissake–"
"Relax," I said. "Nobody's making any cracks about your goddam religion." I got up off Ely's bed, and started towards the door. I didn't want to hang around in that stupid atmosphere any more. (7.50-54)
Holden is right—he isn't making cracks about the religion itself, just like he doesn't really make cracks about education itself. What he's criticizing are the people inside the institutions, the phony people who use organizations for their own purposes.