Aisia from Da Capo Second Season starts off believing that the ability to use magic is so common that the school Asakura attends must be an academy for teaching magic. Obviously she is wrong.
Goku of Dragon Ball thought that every boy has a tail. Amusingly, when he tells Bulma, she gets upset that she still doesn't know about the male anatomy at her age.
When the group needs to get across a deadly booby-trapped hallway, Goku and Krillin easily jump across. Goku says to Bulma it's her turn, and Bulma angrily yells that there's no way she can jump that far. Goku is surprised.
Gohan tries so hard to blend in with normal high school students. Then he jumps thirty feet in the air while trying to play baseball like they do- and then throws a bee-liner to third base to double-off a guy with a two foot lead while everyone is staring at him in shock, and he manages to knock the third-baseman down with the force of the throw (which he was being careful to throw "slowly").
Nanami Jinnai in El-Hazard: The Magnificent World is immune to illusions, but doesn't detect them, so when she happens to warn her friends about one, it's through blind luck ("I thought everyone saw what I did")
At the beginning of Hunter ◊ Hunter, Gon doesn't seem to know that most people can't follow a person in the middle of a forest by the scent of their aftershave.
Tiger & Bunny's Keith Goodman sometimes forgets that other people can't fly
Keith: Why are you hesitating? Get up here! Ivan: I can't! Keith: Why not! Remember, you said you'd do your best! Ivan: I don't have flight. Keith: ...Ah, that explains it.
Envy: How can you use alchemy here?! [Scar and May glance at each other] Scar: ...what do you mean?
Ao in Eureka Seven AO has the ability to see trapar particles, which are invisible to the naked eye. He always assumed they were part of the wind and that everyone could see them.
Cleverly inverted in One Piece. When Luffy becomes friends with the inhabitants of Amazon Lily (who are all woman by the way) each and every one of them think that Luffy is the poster boy for men. Their logic being that since he can stretch, other men must be able to stretch as well
In his honeymoon edition, Spider-man mocks the idea that he created his web fluid and thought any idiot could do the same, but Fireheart's scientists made one that breaks easily.
Aquaman in the JLA Year One series expresses this. He doesn't think of his abilities as powers because everyone can do it where he comes from. Likewise, Martian Manhunter thinks of his abilities more as "skills" or "gifts of will" rather than powers.
In the My Little Pony fanfic The Son Of The Emperor, Twilight is surprised by the fact that something as mundane as lifting books or opening a door with magic is unheard of outside of Equestria. This is because unicorns are not allowed to practice magic beyond certain strict limits, and most of them can't perform even the most basic tasks.
In Serpentine Harry turned out to have a rare Potter family ability to animate his own artwork. When questioned he said "I thought lots of people were able to do that."
In The Student Prince, Merlin doesn't realise that his magical ability is extraordinary even among sorcerers. He can stop time, expand his mind to cover thousands of miles and talk to Kilgharrah, and it's only when Gaius and Morgana tells him that he learns how unusual such talents are.
Rashmika from the Alastair Reynolds book Absolution Gap is a Living Lie Detector. Until her late teens, she never lies, and becomes known for it in her village. It's not for any moral reason, though; she just assumes everyone would be able to tell if she did.
In the Dragonriders of Pern series, F'lar chastises Lessa for not telling him that she can hear the telepathic speech of other people's dragons. Her response boils down to "How was I supposed to know you couldn't?" She simply assumed that it was her dragonrider ancestry that accounted for it, and that all dragonriders would have that ability. Even after she'd been living in the Weyr for some time and had met other dragonriders, the subject just never came up.
Until the middle of Harry Potter and the Chamber of Secrets (when he does it in front of an audience for the first time), Harry assumes that all or most wizards can talk to snakes — in fact, he doesn't even realize he's speaking a different language when he does. In the sixth book, it takes him some time to understand than Morfin Gaunt is speaking Parseltongue in the Pensieve Flashback, as he only hears it as perfect English.
Not an innate ability, but when Harry is told the legend of the Deathly Hallows, one of them is a mythical cloak which granted the wearer true invisibility and never lost its power... which Harry soon realizes is the cloak he'd had since his first year at Hogwarts, and had always assumed was an ordinary (if rare) magic cloak.
Ayla from Earth's Children has an exceptionally well-trained memory for a Cro-Magnon. Of course, she was still considered to be "slow of memory" amongst her adoptive Neanderthal tribe. But once she is amongst her own people, they are constantly baffled by her surprising memory. Oh, and her ability to detect lies from body language. And her advanced gifts as a healer. And her domesticated animals. And...
In the Foundation series, the Mule briefly mentions that it took him a while to realize he could control people's emotions, and even longer to realize other people couldn't.
In Robert A. Heinlein's Stranger in a Strange Land, Valentine Michael Smith thinks that all humans have his mental powers of making objects hover in the air or disappear; he doesn't realize that the abilities taught to him by the Martians are not known on Earth.
In Hopscotch by Kevin J. Anderson, Darragon doesn't realize during the early part of his life that most people can't see auras. The subject only comes up when he notices a Body Swap, so this is closer to being justified than most examples.
Early in the Ciaphas Cain books, he neglects to mention what his tunnel instincts are telling him because it doesn't occur to him that his companion can't tell. He's aware that it's a talent not everyone possesses, it just seems to slip his mind for a moment. Further complicated by the fact that during his childhood on a Hive World, everyone did actually have that same tunnel sense due to living underground.
It's mentioned that Susan thought nothing of her ability to walk through walls make herself unnoticeable, and assumed for the longest time that everyone could do that. Even in her second appearance (by which time she knows her origin), she finds stopping time to be so easy that she wonders why ordinary people can't do it. This is partially justified, in that many of Susan's (and Death's) "supernatural" abilities really are much more straightforward than the way regular humans approach reality. For instance, itís not that she can see things that arenít real, itís that everyone else can not see things that are.
Tiffany Aching knows that being able to step out of your body and look at it from the outside isn't an ordinary thing for a human to do, but she's not sure if it's an ordinary thing for a witch to do. (It isn't.)
Jeremy Clockson in Thief of Time not only doesn't realize that not everyone can intuitively tell what time it is, but he doesn't even seem to grasp that that's what the clocks he devotes himself to crafting are used for.
Brutha from Small Gods never forgets anything, never has dreams, and always knows his exact location on land. He eventually does realize that the former isn't true of everybody, yet the concept of "forgetting" remains extremely perplexing to him.
It's a more mundane ability than the above, but in Jingo an impressive display of juggling and other street theater tricks leads Colon to say to Vetinari "I didn't know you could juggle, my lord" and Vetinari to ask "Can't everyone?" It may just be a reference to how good Vetinari is at keeping everything going where he wants...
Justified for Ax of Animorphs in that he's not human, but he's rather surprised when he learns that humans cannot tell time accurately or judge direction (North-East-South-West) innately. (Of course, with only a little training, they can.)
Fitz's daughter Nettle in the Tawny Man trilogy is a DreamWeaver, but doesn't realize that this is anything special. She doesn't understand why other people have nightmares, because why would anyone want to stay in a dream they didn't like?
Like a lot of folks, he has a knack and doesn't even know it because that's the way knacks work: it just feels as natural as can be to the person who's got it, as easy as breathing, so you don't think that could possibly be your unusual power because heck, that's easy. You don't know it's a knack till other people around you get all astonished about it or upset or excited or whatever feelings your knacks seems to provoke in folks. Then you go, "Boy howdy, other's folks can't do this! I got me a knack!" and from then on there's no putting up with you till you finally settle down and get back to normal life and stop bragging about how you can do this fool thing that you used to never be excited about back when you still had sense.
Warrior Cats: Dovewing says this word for word when she finds out her super hearing is a special power.
Honor Harrington isn't modest enough not to realize she's an outstanding military commander, but has difficulty believing that when she pulls off some kind of awe-inspiring feat (such as the mass prison escape from Cerberus) that people don't accept it was merely her duty to do so and thus she deserves no special accolades for it. She also has no idea how inspiring she is: she's astonished to learn that people who have served under her end up, on average, being better officers than their peers afterwards.
Invoked in the X-Wing Series. When reforming Rogue Squadron, Wedge chooses one pilot over another to join the squad as his executive officer, even though the pilot that's suggested for him is renowned and the pilot he wants is a suspected traitor who will have severe restrictions placed on his behavior. Later, attrition catches up to Rogue Squadron, and he brings the other pilot in, though not as his XO, and explains to her that he's seen her fly before. Her skill as a pilot, he believes, can't be taught, and what he needs from his XO is, among other things, a trainer. Picking her would result in her being frustrated and his pilots bewildered (and possibly dead). But now there's room on the squadron, she's definitely earned a spot with her skill.
In Sikozu's first appearance, she's rather surprised to discover that Crichton can't shift his centre of gravity, having presumed that all the species she had associated with so far (Scarran, Grudek, Sebacean, Human) were able to do so. Unfortunately, she only finds this out while bandaging Crichton's mauled legs — courtesy of the Monster of the Week Sikozu had easily escaped from.
In another Farscape example (though this time more of "I Thought Everyone Couldn't Do That''), Crichton discovers that every member of Moya's crew has better eyesight than he does when he claims there's nothing written on a basin, and the others take turns reading the small warning text aloud.
Pilot didn't know that everyone can't see the bubble of an emerging wormhole until Crichton mentioned it was invisible. Crichton can "kind of smell it", but this is known to be a unique ability.
Fonzie of Happy Days is convinced that he's been given a class of subnormal students because they can't change a carburetor perfectly after being shown how once, as he was able to as a boy.
Hyde in Jekyll. He knows that ordinary people aren't as strong or fast as him, but is still surprised when he learns that Jackman can't do things like detect drugs in his bloodstream or pull up photo-quality images from his memory.
"There's something new in our bloodstream, keeping me awake. Tickles." "You can feel your blood?" "You can't do that?"
Jack: Dennis, how did you not KNOW? I mean, hadn't you ever seen other guys in the shower? Dennis: No, I sat gym out because of my allergies. The only time I saw other guys naked was in porn. I just thought I was a little above average.
Humorously, this is actually a rather wide-reaching (if funny) retcon; previous episodes had definitively established that Finch was on the extreme other end of the size scale, and was once confused for a woman when he was seen in a skin-tight bathing suit. For most of his life (until this episode) he really wasn't extra-big.
Parker of Leverage makes a quick and accurate sketch of a hit man who's been following their mark around.
Hardison: Wow, I didn't know you could do that. Parker: I thought everybody could do that.
Truth in Television. Word of God is that Parker has Asperger's, and some people in Real Life with Asperger's or Autism can make extremely-detailed drawings of things they only glimpse once due to their brains focusing on these details at the expense of other things.
In a sketch on MADtv, recurring character Rusty Miller, a geeky college student, is having a trivia contest with two girls, and infuriating them by getting every question right. Except the last question, which asks the average length of a penis. The girls get it right by answering six inches. Rusty protests that the machine is wrong, and the average is ten inches, then leaves the bar in disgust. The girls give each other a look, then rush out after him. As do several guys.
Used to dramatic effect in Six Feet Under. Brenda explains that when she was little, she read a report about the possibilities of a nuclear war breaking out. She explains that from that point on, every morning she woke up, she would feel thankful for being alive, yet also feel closer to nuclear apocalypse. When Nate asks how she could live like that, she says she thought that's how everybody else lived. Of course, she's not entirely wrong; there was in fact a lengthy period in recent human history where anyone who paid more than superficial attention to international relations really did live like that, and with good reason.
In "The Prime Mover", an episode of The Twilight Zone, Buddy Ebsen plays Jimbo, a man with telekenetic powers who explains that when he was young he believed everyone had them. He only stopped using his when he found out that wasn't so, since he'd done a few things that had gotten him in trouble.
In the Xenosaga series, Albedo is shocked to learn that other people can't regenerate, including his brothers. This occurs after a very disturbing scene in which a child Albedo blows his own head off in front of his brothers with an energy blast, or a gun in the Japanese version. For great Mood Whiplash, he was only trying to be funny.
In Mass Effect 2, Wrex doesn't realize that humans don't have a redundant nervous system like krogans and thinks that it's the explanation for how Shepard was able to survive being spaced when the Normandy was destroyed until being informed otherwise.
In Digger, Shadowchild is surprised to learn that not everyone can transform into large, demonic-looking monsters at will.
In Girls in Space, Zoe doesn't mention to her employment councilor that she's an omniglot, because she thought everyone on Earth spoke all Earth languages.
Celia from The Order of the Stick designs her summoning talisman to break from energy blasts, completely unaware that this was not something normal humans could do at will, which leads to some unfortunate consequences when her boyfriend fails to use it. She can also detect abjurations like the Cloister spell through the way her teeth tingle. Because she thinks everybody can do the same, she only mentions it in passing, assuming Haley already knows about it; when she finds out Haley doesn't, she actually gets angry about how worthless human(oid) senses seem to be compared to her own.
For a while in Sluggy Freelance, Aylee keeps forgetting that earth creatures need things like sleep and oxygen to survive, and don't have quite her ability to heal.
SCP Foundation: SCP-1454 is a set of four identical men who have a shared memory. They see nothing unusual about this; as far as they know, it's perfectly normal for a human being to have memories of working over 200 hours per week and having had more than one first kiss.
In an episode of The Alvin Show we meet Dave's country cousin, Chuck Wagon, who claims he can't do anything. Alvin Simon and Theodore decide to help him find some sort of talent, all of which fail miserably. They and Dave are later astonished to find him playing Theodore's guitar and singing about how he has no talent. As it turned out, where he came from, everyone could play the guitar and sing so it never occurred to him that it was anything special.
In the baseball episode of Doug, Doug didn't realize that being left-handed meant he should swing from the other side of the plate when batting compared to right-handed players. Once someone else realized this and told him to change his position, he immediately went from being the worst hitter on the team to getting a run scored with his next swing. He thought he was just bad at baseball.
As a child, Julian Asher, the famous neurologist and synesthesiac, assumed that the lights are dimmed during a concert so that the audience can see the light that emanates from the music better.
The documentary program The Science of the Senses described a man with face blindness who never realized how different he was until late in his life, when his mate told him that all the "confusing" close-ups in films (for him, the characters become unrecognizable if he can only see their faces) aren't actually confusing for ordinary people.
A man who underwent a psychedelic experiment in hearing through the mouth was stunned to learn it was unusual that he has heard multiple noises pulsing through his head his whole life. He once was terrified by the concept of true silence, and he used to take sayings like "Your silence is deafening" as more literal than ironic.
This is related to the common phenomenon known as "illusion of transparency", where you assume that others can accurately read your experiences and emotions because you already know it. Also known as You Know What You Did.
St. Pio, also known as "Padre Pio", spent his childhood thinking that everyone got visited by angels and saints on occasion.
People with Asperger's Syndrome might grow up thinking this, especially if they are not diagnosed. Though this is less "I thought everyone could do that" and more "I thought everyone else thinks the same way I do".
It's theorized that one reason that some star athletes have a hard time getting along with their teammates and come off as aloof and argumentative is that they don't understand they're just that much better than the average player in the game. They tend to assume everyone else around them is slacking, or unmotivated, when the reality is they just can't play as good as the star no matter how hard they may try.