As the son of DC's greatest hero, Jonathan Kent was a popular addition to the Superman mythos, adding a new dynamic for Clark Kent as he balanced not only being a hero and a reporter, but also a father. But one decision would rob him of watching his son grow up in a (relatively) safe environment. The amazing person he and Lois Lane raised would return to them in time, no longer a boy, but a young man. But even though both parents are proud of the person he has become since then, they still grieve the time they lost with their son.
This all started with an offer from Clark's side of the family. Jor-El appeared before the Kents, and offered to take Jon on a summer trip through the stars to broaden his horizons and increase his knowledge of the universe. It was a chance for Jor-El to give his grandson the formal education his own son never got.
Jon surprised his parents by wanting to go on the trip. He had been having lingering doubts about his status as the son of Superman. He was afraid he wouldn't be able to live up to the great legacy his father would one day entrust to him. His hope was that by going on this trip he would be able to discover himself, and what kind of hero he would be outside of his father's shadow. His parents had concerns, but Jon's enthusiasm and honesty eventually won them over.
Still, they didn't feel they could just trust Jor-El with their only child, and since Clark couldn't just leave Earth all summer, Lois volunteered to go into space with her son and father-in-law. The family bid their farewells, not realizing that the trip would vastly change Jonathan.
Lois quickly realized that she couldn't keep up with her son or his grandfather. In space, she wasn't as useful as she could be back on Earth. She made the decision to trust Jon's judgement, leaving him with Jor-El while she returned to Earth in secret, beginning to secretly write her book about her life as Clark's wife. But that decision, on top of the one to allow Jon to go on this trip, would later haunt the Kent family.
Jon and Jor-El traveled the stars for a time before they were sucked into a black hole. Jon wound up on Earth-3, the home of the Crime Syndicate, where he was captured by Ultraman, who imprisoned Jon in a volcano and used him in a sort of therapy session. This went on for years until Jon found a way to escape before finally being rescued by Jor-El, who sent him back to Earth. To Jon's surprise, although years had passed for him, it had only been three weeks since he left Earth.
In Superman #6, by Brian Michael Bendis and Ivan Reis, Jon revealed himself to his parents. Although relieved to see him alive and well, the Kents were heartbroken by the years they lost with him. Jon had been ten when he left home and had come back seventeen years old. They had lost almost a decade with him, time they could have spent raising him in a much less emotionally traumatizing environment. They were robbed of raising their child because of one decision they made.
But they could at least take comfort in knowing that what lessons they did manage to impart in their son kept him alive during his years away from them. The hope, courage, and compassion they instilled in him allowed him to survive years of torture at the hands of a madman and return home stronger for it. However, they will always mourn the little boy they lost in the process.