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People can perceive poor people skills as being harsh or mean. "Cruel" is a word that carries a connotation of enjoying causing others pain, I wouldn't go quite that far.

But some people have very low "EQ" or emotional awareness, they are emotion-blind to others, and don't realize that when they are blunt or honest they are hurting other people's feelings. Even when they do it, they can't read the hurt expressions or voice tones in other people. IRL, some with severe forms of this disability cannot tell the difference between a person laughing and a person crying.

That is at least one way around the problem. Such people can seem like they don't care about others, while they actually do, and then their actions will speak for them. They do take action, sacrifice their time and money to help others when they perceive a need, or are asked.

A common plot device for such characters is their help is requested by somebody weak and desperate, and they step up. A child or teen, perhaps, or on the opposite end but still helpless and desperate, an elderly person.

Such people are often both loners and lonely, an inability to perceive emotions in other people is a disability that makes it difficult to form close friendships or romances.

I like this version of the question better than the last one.

There are many ways to be considered a jerk. The most common is someone who deliberately says or does things that are cruel or obnoxious. But another is to be unthinking about people around you. You might be off in your own head, or have difficulty hearing or seeing so you just nod along, or have a disability that interferes with your ability to connect, or just distracted. These things don't make you a jerk, but they can lead other people to think you are.

Your character might not pick up on subtleties very well. This can make him sound harsh when he's only answering a question or stating something that is factual.

He may have been raised with harshness so he echoes the language.

He may, as you suggested elsewhere, be struggling with a trauma that is blunting his emotional response and/or making him unaware of other peoples' difficulties or reactions.

The fact is that everyone is a jerk sometimes. None of us is perfect and we all have character traits that other people dislike. It's also common for people to behave worse when they are under stress.

Given that, it should be fairly easy to paint someone as a jerk simply by looking at the times they screw up, or by focussing on them when they are in a highly stressful situation and not behaving as they would normally.

It's very easy to gain an opinion of someone based on just a few events; that opinion is likely to be incorrect or at least only partially correct, but it can also be very difficult for someone to shake off a bad first impression.

In theory it is a simple as having him do something that looks really callous or bad and then developing or revealing a back story that absolves him of the moral crime.

Jaime Lanister - the Kingslayer - from Geroge R. R. Martins A Song of Ice and Fire does this almost perfectly. He is hated, or at least dishonoured, for essentially saving the lives of millions of people. If you could take inspiration from this character's arc I think it would fit your needs.

This is very much a point of view question. People misjudge people all the time, because they see them from their own personal perspective. If you want a character to seem like a jerk, then see him or her as a jerk from the point of view of your viewpoint character. That character, in turn, could have a wealth of reasons for the misjudgment --personal prejudices, misunderstandings, being overly sensitive, reacting negatively to sexual tension, and so forth.

You can make this easier by giving the misjudged character some superficially off-putting characteristics, particularly ones designed to trigger the viewpoint character's prejudices. Is the misjudged character ugly? Shy or reserved? Loud and brash? Wealthy? Poor? Whatever it is, have your viewpoint character focus in on some disliked detail to the point of not being able to see the full picture.

Of course, it's much harder to make this not seem like a cheat if you have a third-person omniscient narrator. In that case, you might want to give the "misjudged" person some actual flaws he or she can overcome in order to deserve a re-evaluation.

One method I love is the "Same Goal, different Motive" for characters. Suppose your POV and your "Lancer" (From TV tropes article describing heroes that run counter to the definitive good hero/leader) have come to the conclusion that they have to complete the same goal, but must do so for two very different reasons. One immediate example that jumps to my mind is the (as of time of writing) ongoing Super Sentai Series "Lupinranger vs. Patoranger" (Super Sentai is the source show for the American show Power Rangers... they tend to use the same costume in a given year, but different casts to play the heroes out of suit).

The current series is unique in that it starts with two ranger teams hunting the same treasure for different reasons. The first team, the Lupinrangers are hunting down the treasures because the owner of the collection promised to help save a personal relationship of each member who is a victim of the monster group for this season. The second team, the Patorangers, also want the treasure because they are police officers and the treasures component pieces are allowing the monsters to endanger the general public. While they have the same goal, and infact, out of heroic duties, they do get along just fine (though the later is unaware of the former's status), in costume, the confrontation does have elements that make both sides look like jerks to the other. The Lupinrangers see the cops as uniformed about the whole situation and have a lot more personal motivation in getting the treasures than the cops. Since they Lupinrangers are doing this with the style of professional thieves, the Patorangers see them as criminals to be arrested, no different than the monsters, and each successful theft of a new piece to be no different than a criminal stealing from another criminal. They also have no personal stake in mission success... it's their task force assignment at the current moment.

This is common in a number of other stories too, and when pulled off, can give proper motivation to incentivize would be allies against each other. Consider the following motivations: I must stop the bad guys because they kidnapped a familial relation vs. I must stop the bad guys because they will hurt people. Both are good motivations for a hero, however, a hero with the former will need to play detective and get the bad guys to give him/her information about where the bad guys are hiding the father. The hero with the later, when confronted with the fact that the other hero isn't out and out stopping the bad guys, is not intervening in lesser crimes, or is even talking to them and offering them safety, may not think for the motive and see the former hero as ineffective at best OR even a threat to his/her mission at worst.

In Californication, David Duchovny's character is an essentially well-intentioned writer who repeatedly draws the ire of his daughter and baby momma due to his hedonistic dalliances. But often, there is an accidental component that he gets blamed for because they attribute intentionality to it. For example, sleeping with an underage girl who he didn't know was underage. Second example: circumstantially looking like he slept with someone he didn't sleep with. He also slept with his daughter's boyfriend's mother and didn't know she was his mother. There were probably at least 20 times they were mad at him for doing something he didn't do, didn't realize he was doing, only appeared to be doing, or shouldn't be blamed for.

In My Hero Academia, there is a character named Iida who aggressively corrects a speaker leading an orientation. He immediately seems like a hostile jerk. Over time, it turns out that he is a very type A personality, regimented, rule-abiding class representative.

At any rate, misunderstandings and highlighting the most extreme, non-representative part of the character's personality seem to be the way to achieve this.

In addition to the other answers: Body language and impression by looks can have a huge impact on communication. Especially as it is understood subconsiously by most people.

So the same words of a character that looks very grimm or scary and has the body language of a dominant person will be received different than from a soft looking, relaxed guy. Because for our subconsiousness first impressions are important.

You can combine this for example with speaking few words because of lacking communication skills.

For example lets have an old war veteran:

Bob has a big scar in his face (even lost his eye) and is living alone
in his hut. Bob is dominant and blunt, he walks with the gait of a
fighter and looks people into the eyes directly, forcing them to look
away. His combat ready stance lets the villagers feel uneasy in his
presence. Their subconscious tells the them that he is dangerous so
they avoid him on instinct.

What they don't know is that Bob acts like this because of all the
years in the war where he had to distinguish foe from friend. Habits
die hard. You are more cautious when you have to look over your
shoulder every day. You look at each corner in anticipation of danger.

He is used to interact with other warriors so he has no clue how to
handle women - as result he acts harsh out of confusion.

In real life, I have changed my opinion several times about people I've known. A couple of examples:

I met a guy who seemed a callous jerk; he later appeared to mellow out, and I learned that when I met him, he'd been grieving the loss of a family member. The grief brought out a savage edge to his sense of humor that dulled as he recovered from the loss. We became better friends.

At one point I met a group of people, and made a snap judgement that I liked Friend A the best. A described Acquaintance B's cruel traits and actions, so of course I kept my distance from B. Only after some time did I discover that A was manipulating the group to isolate B; A was the jerk and B the innocent victim. This was hard to accept, since I liked A so much, but narcissists can be charismatic and convincing at first. Unfortunately by this point B wanted nothing to do with me, and several friends had judged that I too was a jerk.

None of us are perfect judges of character. Look to your own life for cases where you've misjudged, and you'll be able to write both the misunderstanding and the aftermath convincingly.

Give them their own agenda & make them act according to it, but don't let the MC / audience know of their hidden agenda, until you are ready to get to the "eventually they find out he isn't such a jerk" part - preferably find it such that occasionally in odd ways they don't act as would be expected of a true jerk (i.e. sometimes their hidden interests coincide with the MC, thus they may end up helping, or at least not hurting their efforts) - there have been some examples given already, but I would add Snape from the Harry Potter series would be a good example of this done successfully