Fathers get this treatment as much as any other family member, but that doesn't mean they're all bad. In fact, incredible fathers and father figures exist in comics. Marvel, DC, and Image Comics have all presented examples of dedicated fathers. Their children have all benefited from their love and teachings, becoming better people.
Superman has long been DC's greatest role model. He's always been the father of the superhero community, giving advice and guiding them whenever he could. His marriage to Lois Lane would eventually lead to a child. Jon Kent was lucky in that he had the best parents any kid ask for: the world's greatest hero and the world's greatest journalist.
Superman used what Pa Kent taught him as an example. He loved Jon more than anything and wanted him to succeed. He gave Jon valuable advice, and Superman proved the perfect person to show Jon what it takes to be a hero.