Why do you think Mr. Gold hates nuns?

Because their Fairytale counterparts are Fairies. And as we saw in flashbacks, Rumple killed the Fairy Godmother. So it's likely that either the Fairies retaliated after he did that or something happened prior that we haven't seen yet, that he's still angry about.

Probably something to do with the fairy tale land. Maybe they get him to see his wrong doings and he doesn't like it.

I think he might hate the fairies (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 said "No one can EVER love me!" to Belle!

It could be because the nuns were fairies in FTL and he blames the Blue Fairy for taking his son away by giving him the magic bean to send him to 'the land without magic'.
I don't know if that makes a lot of sense.

Maybe cause he is "magical" and nuns think his "magical type" is bad.

Nuns used to be fairies. It was a fairy that came up with the spell that inprisoned Rumplestilskin.
(the name looks wrong, but you know what I mean)

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 fairies 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.