In early appearances, there was not a lot of consistency about what exactly the symbol on Jor-El's chest looked like. Most commonly, it seems to be a sun-like image (often with a jagged red rim), but a ringed planet inside a yellow circle was also frequent.
... versus ...
This kind of imagery seems to be used mostly to remind us that Jor-El is from outer space.
Originally, Jor-El had no image at all on his chest. Here are his earliest appearances, from 1939 Superman newspaper strips.
The earliest representation I am aware of that has him with something in the center of his chest is this Sunday newspaper strip, where it's just a yellow ring.
And using Google image searches, you can turn up examples of Jor-El with other chest icons as well, such as a plain yellow triangle.
The idea of having Jor-El wear the S crest originated with the 1978 Superman movie.
However, the idea that Kryptonians (or at least the males) typically wore clothing with chest symbols is quite a bit older. This is apparent in the full page image of the, "Gentlemen... Krypton is doomed!" frame above.
Ultimately, it seems that the visual reason for placing some kind of icon in the center of the chest may have simply been mostly to make Jor-El's appearance more closely mirror that of Superman. Since a lot of superhero characters have symbols in the centers of their chests (largely following Superman's example), it makes Jor-El look "superhero-like" to also have a sigil there.