They also gave the FBI the last iCloud backup of the phone (a month before the attack happened), so it's not like they haven't cooperated with the FBI at all in that case. It's just that it wasn't enough to the FBI, and that's where Apple drew the line.
Apple is clearly working toward securing that data so they can't supply it in readable form. Hard to reconcile that with excellent usability & UX, but they're solidly heading that way. Encrypting that iCloud backup such that it [mathematically] cannot be used without the Secure Enclave is surely coming. To wit: "here's all the data we have, only the defendant can unlock it, and no we're not building backdoors in."
The trick, of course, to preventing government surveillance is for companies to just not have the data in the first place.