Technically, grammatically, I suppose that might be OK, but semantically as a native speaker I would never say It rains? by itself as a question. If I wanted emphasis, I might say something like - It rains in Vancouver? REALLY?????, but I'd have to have something following the it rains.
Note: I found that Duo is translating Het regent as a statement as It rains. This is somewhat more acceptable than it rains? alone as a question, but I still miss something after the rains. Needs a duration, a place, a quantity, an object of some sort (Sometimes it rains frogs after a tornado)
Regarding Het regent:
You feel uncomfortable with the bare "It rains" because English is far more progressive-happy than Dutch. "It rains" sounds very atemporal, like it's a universal truth that rain always happens. "It is raining" is much more natural sounding because it provides a time aspect—right now—and English sentences often want some sort of time specified. Dutch is okay with this arrangement because the use of the progressive aspect is deemphasized and the simple present tense works just fine to adress what is happening right now. That being said, either English translation is acceptable because they both would translate back into Dutch as "Het regent".