To protect his face
He may be indestructible, but there are other indestructible things and beings in the DC universe. On top of that, invisibility is a thing. If he's going to crash against Wonder Woman's invisible airplane midflight, it'll hurt less if he hits with his fist than if he hits with his face.
Ever got your arms out of the window of a moving car? I feel the windy senstion is really pleasant. Maybe Kal-El just likes the way the air moves around his arms as he flies.
He's mimicking a swimmer
When athletes jump in the water, and in at least one swimming style athletes will keep their arms in front of them like that. Not only that, the whole body position is similar. The difference is that Kal El looks head instead of downwards and sometimes he makes fists rather than having his palms open.
Maybe he saw people swimming before and he originally thought flying was like swimming in the air. That stuck with him and he never had any reasons to change how he flies. Compare with Marvel's doctor strange, which flies purely by magic, and also Marvel's Thor and the little prince, which fly by holding on to magic tools.