Even for a serial it's cheap. In a live action superman adaptation you should see a live action superman flying imo.
But Superman Returns
used a CGI Superman for the flying scenes, and the Spider-Man movies use a CGI Spidey, and the Matrix
movies used a CGI Neo, etc. The animated Superman in the '40s serials was the exact same principle, just with less photorealistic technology. Back then, people weren't as nitpicky about the realism of their visual effects as we've become. Images that look blatantly fake to us were impressive and convincing to them.
The "flying" Captain Marvel in the serials was just a motionless life-size dummy sliding on a wire in a straight line. The animated Superman of the serials flew with much more speed, dynamism, and fluidity. I think the latter did a better job of conveying the idea of what the hero was capable of, and that's more important to me than whether it was live-action.
And what makes you think it's cheap? Animation is a laborious, time-consuming process. And good animation, as you acknowledge this was, takes even more time and talent -- and therefore more money -- than bad animation. Not to mention the added complexity (and therefore cost) of compositing cel animation with live-action footage. It was probably a lot more expensive to animate those flying sequences in the Superman serials than it was to make a dummy and slide it down a pair of wires.