I'm creating a cleric of Erastil and I'm thinking about choosing the Good domain and Feather subdomain. Should the Fly skill be the only class skill gained or is it supposed to supplement the Knowledge (Nature) class skill gained from the associated Animal domain?
You get both.
the convention is that you get everything from the super-domain except for the features the sub-domain explicitly says get replaced.
I couldn't find any great sources to cite. This is the closest I could find:
It makes sense to give fly in addition to Knowledge(Nature) because you still get Animal domain powers/spells but the fly skill is also needed because you now have access to the fly spell.