resurected Jesus?
Shoeless Joe Jackson et al in Field of Dreams.
Ghost? Whoopi Goldberg & Patrick Swayze?
As opposed to non-fictional Characters? 
My small contribution: The unicorns of the book and movie, “The Last Unicorn” are seen as just horses by most.
In one of my favourite anime, Kamichu!, the local god Yashima-sama can only be seen by the younger shrine maiden Miko Saegusa (and not by her older sister Matsuri), and not by other human beings – though the central character Yurie Hitotsubashi can see him, of course, since she is a god as well as a middle-school student.
And later on Six started hallucinating her own Baltar. And now Baltar is hallucinating a Baltar.
The Lectroids from Planet 10 could be seen by everyone, but not as Lectroids. Then only a few people from the Banzai Institute could see them as Lectroids once Buckaroo was zapped with the chemical formula for the antidote gas.
The “family ghost” of the Remillards in the Galactic Milieu series can only be seen by Rogi Remillard.
Gary Coleman had a short-lived cartoon, The Kid with the Broken Halo (based on a TV movie with the same name). In the cartoon, his character was the only one who could see the villian, Hornswoggle.
In Lost, only Hurley could see his former fellow inmate Dave. Later, Hurley saw the ghost of Charlie, and apparently was the only one who could.
Only Jack could see his father.
Many other examples over the course of the series.
There’s also Jennifer, the ghost played by Ann Jillian in the short-lived TV show, Jennifer Slept Here.
In the short-lived Nickelodeon show Space Cases, only Catalina (played by a pre-Firefly Jewel Staite) could see her imaginary friend Suzee. Later, Suzee and Catalina switched dimensions and the reverse was true.
On Buffy, the First Evil could manifest to only certain people as it chose - it ‘haunted’ Angel and Buffy couldn’t see the people talking to him, and later on it did much the same thing to Buffy, and Andrew, and Spike.
Well, in a few episodes, Marty Hopkirk could be seen by psychics, people in a hypnotic trance, or (IIRC) a guy who was extremely drunk. (And, of course, other ghosts could see him … one episode has him getting a message to the real world by talking to a guy [patient undergoing surgery] who’s having a near-death experience … )
I am, of course, referring to the original ITC series, and not the abomination that was the Reeves and Mortimer remake.
Only William Shatner could see the creature on the wing of the airplane.
Not true. John Lithgow: The same thing happened to MMMMMMEEEEEEEEEEEEE!
Only Whoopie Goldberg could see Patrick Swazye in Ghost.
And, damn, we was cheated outta that Whoopie/Demi make-out scene.
Ooh! Here’s one! In an episode of MASH,* only a fevered, delirious Klinger could see the ghost of a young soldier haunting the 4077th.
Most of these are going to be ghosts, aren’t they?
Here’s another. Only Andrew McCarthy’s character in Mannequin could see his girlfriend as anything other than a mannequin.
In the short-lived Raines only Jeff Goldblum’s titular character could see his dead partner (wow, I never realized how common a theme that was).
On the Discworld, only cats, witches, and wizards can see Death, unless he, or some magic, allows them to.
Don Knotts, only Mr. Chicken saw the Ghost.
…and any number of scooby doo episodes. Often it was just Scooby and Shaggy who encountered the Ghost.