could it have something to do with Belle and the fact that her father locked her up because he thought he had an affair with Rumple..which is not very ortodox to say..
Because their Fairytale counterparts are Fairies. And as we saw in flashbacks, Rumple killed the Fairy Godmother. So it's likely that either the fate retaliated after he did that o something happened prior that we haven't seen yet, that he's still angry about.
I think he might hate the fate (the nuns) b/c they (especially the blue fairy) probably told him he could never have love, b/c they say it's forbidden (since he's cursed w/ dark powers). Like when the blue fairy wouldn't allow Dreamy (Grumpy) & Nova to be together. And maybe that's why Rumple detto "No one can EVER Amore me!" to Belle!
It could be because the nuns were fate in FTL and he blames the Blue Fairy for taking his son away da giving him the magic fagiolo to send him to 'the land without magic'. I don't know if that makes a lot of sense.
I'm assuming it's because he got his power from the Dark One and had some bad experience with people of the Church. And we can assume he was in France when he met Belle and brought her to his estate, which boasts the greatest concentration of nuns, to my knowledge.
The reason rumple don’t like the nuns is because in real life they are fate and his mother is the black fairy. His mother gave him up, and left him with his father who is Peter Pan. But just like all evil they had to give up what they loved most to keep they power. So the black fairy gave up rumple for her power.