Here's why:
* Superman's real name is Clark Kent: The name "Superman" is a title or alias that he adopts as his superhero identity.
* Jor-El knew him as Kal-El: Superman's Kryptonian name was Kal-El. This is what Jor-El and his wife Lara called him on Krypton.
* Jor-El raised him as Clark Kent: After sending Kal-El to Earth, Jor-El and Lara entrusted his care to Jonathan and Martha Kent. They raised him as Clark Kent, so he wouldn't be burdened by his Kryptonian heritage.
So, the father, Jor-El, would have called him Kal-El or perhaps "son" in a more familiar context.