I'm referring to the first few minutes of the 1978 Superman movie with Marlon Brando. Jor El comments on the amount of time necessary to travel to earth but Clark arrives here and looks like a 3 or 4 year old.
The discrepancy between Kal - El's age and the 'thousands' of years that has past since Jor - El's demise is a nod to the relativistic effects of high speed long distance space travel.
Einstein demonstrated that time is relative to the observer.
Special relativity 'indicates that, for an observer in an inertial frame of reference, a clock that is moving relative to him will be measured to tick slower than a clock that is at rest in his frame of reference... Theoretically, time dilation would make it possible for passengers in a fast-moving vehicle to advance further into the future in a short period of their own time. For sufficiently high speeds, the effect is dramatic. For example, one year of travel might correspond to ten years on Earth.' (Wikipedia - Time Dilation).
So, due to the incredible speed of the spacecraft he was in, only 2 or 3 years will have passed for Kal - El during his journey to earth while in relative terms, thousands of years will have passed within the (relatively) static locals of Krypton and Earth.
The film script indicates that the boy is 3 years old.
The little BOY, aged 3, suddenly springs out of the electronically controlled belts, half naked.
And there's some confirmation that the module was traveling FTL, at least for portions of the journey
37 EXT. SPACE - CLOSE ON MODULE:
Traveling through space: A tiny yellow dot becomes larger as the module enters our Universe. The yellow dot grows rapidly into a flaming yellow sun.
In most other continuities the Kryptonian rocket is explicitly stated to have a "hyper-drive" or a "phantom-drive" to explain its rapid progress.