Frodo was an orphan that never quite fit in at Brandy Hall. Some JRPG protagonists are left as fairly blank slates (Crono, Link), while Cecil of Final Fantasy IV was an orphaned prince, in Fire Emblem Marth loses his father and sister at the start if his adventure, and while not strictly a JRPG, Samus was raised by foster parents and was genetically modified to be a super soldier.

Sure, not every game or plot followed the trope, and there are plenty of great examples that break the trend or flesh the story out to carry it well, there's a reason "orphaned chosen one" is a trope in the first place.

It's also just something silly to point out and chuckle over. Sure, there are positive, story compelling reasons for a random commoner to be thrust into extraordinary situations and become a hero of the realm! But there's also little (normal) reason for Bob the Baker to leave his life as a staple of the community with a loving family and steady work to wander the realm facing dangerous monsters and delve into ancient tombs. When you find a way to make the later work, it's amazing, though!