Jonathan comes from the biblical name of King Saul's son, Yehonatan, meaning "God has given." Yehonatan was famous for his true friendship with the man who later succeeded Saul to the throne, King David. Unlike many biblical characters who end up sinning against God or other people, Yehonatan's character is pure and heroic.
It is important to note the difference between Jonathan and John, and the difference in the nicknames. People named John often go by John or Johnny, while Jonathans often go by Jon.
Continuing a 20-year decline from the height of popularity, when Jonathan was the 15th most popular name for boys in the US, Jonathan now stands at 30, but it is doubtful that the name will disappear soon.
2010 Update:
A slight rise. The name is now at number 28.
