I don't see what's dumb about it. I mean, the way Kryptonians fly has no good explanation, but we can assume it requires pushing against something, whether it's the air or the Earth's surface or the Earth's magnetic field or something. Just magically moving in vacuum without any source of thrust makes no sense. A human-shaped being flying in the atmosphere doesn't make much sense either, but it's slightly less nonsensical than flying in vacuum.
Also, I think the Arrowverse follows the precedent of the post-Crisis comics and the DC Animated Universe in having Kryptonians require air to breathe, so they couldn't operate out of the atmosphere anyway.