This answer is subjective and left up to individual readers. The book is a young adult novel, so the author focused on finding ways to make his main characters sympathetic to a particular reading audience. In this case, that audience is young teenagers.

One immediate way to make characters sympathetic to young readers is to have young protagonists. That is the case in this book. Bruno is nine years old, and that happens to coincide with Shmuel's exact age as well. Even adult readers are likely to sympathize with those two characters because adults are likely to remember what it was like being that age.

The story's setting isn't likely to have been experienced by any current readers, so the author puts his characters in situations that resonate with modern-day audiences. For example, Bruno being angry at the move and being basically friendless is likely to elicit sympathy from readers. Readers are also likely to sympathize with Shmuel's loss of family members.

A result of the author targeting young readers is that he has to explain things to young readers. He does this through Bruno's ignorance about a lot of things; however, this does make Bruno less sympathetic to adult readers in my opinion. It is a bit mind boggling how Bruno doesn't know what Jews are, how to pronounce "Furher," nor does he know what "Heil Hitler" means. The fact that his father is so high up in German leadership makes it even more unbelievable.

By 1939, about 90% of German children were part of the Hitler Youth program, so again it seems somewhat impossible that Bruno could be so ignorant, and that makes him less sympathetic in my opinion.

John Boyne creates sympathy for the characters Shmuel and Bruno throughout the novel by placing them in challenging situations and surrounding them with difficult people. Boyne chose to depict Shmuel as a sickly, skinny boy who is typically sad throughout the novel. The reader feels sympathy for Shmuel's difficult situation, and his physical appearance. Shmuel is often hungry and scared throughout the novel. He explains what it is like living with eleven people in one room, and recalls how his family was separated. Boyne also creates sympathy for Shmuel by putting him compromising situations, like when Lieutenant Kotler beats him for supposedly "stealing" food from Bruno's fridge. When Shmuel tells Bruno that he lost his father, the reader feels sympathy for his character because they can assume Shmuel's father is dead.

Boyne creates sympathy for Bruno throughout the novel by placing his character in an unfamiliar, dreary environment in the middle of nowhere. The reader feels sympathy for Bruno when he comments on how bad he hates his new house, and how he misses his friends at home. Bruno lives with his difficult sister and has to deal with Nazi guards who treat him with contempt, like Lieutenant Kotler. Bruno does not get his way throughout the novel, and is forced to keep his best friend a secret. The reader sympathizes with Bruno's difficult circumstances when he cannot play with his only friend. Boyne creates the utmost sympathy for both characters when they unknowingly are being led to the gas chambers. By juxtapositioning the innocence of childhood with the inhumane conditions of a WWII concentration camp, readers begin to sympathize with these helpless children stuck in a horrendous circumstance.

In The Boy in the Striped Pajamas, how does Bruno's opening scene show innocence?

During childhood one only knows life through the medium of family. One child lives in a certain kind of house, he has a certain number of family members, he has a father with a certain job, and there may be certain customary activities that they observe. Life is simplistic. Young Bruno knows only these basic facts about his friends; he is not concerned with anything else because his focus is merely upon his interaction with the other boys. When they talk, it is probably about their teachers, classmates, friends and what games they will play. They are innocent and unaware of what historical moments are being played out in their time.

About the other boys' fathers, Bruno simply knows from hearing them tell of their fathers at school that Karl's father is a green grocer, which Bruno knows is true "because he ran the greengrocer's shop in the centre of town"; Daniel's father is a teacher, which Bruno knows is true "because he taught the big boys it was always wise to stay clear of"; and Martin's father is a chef, which Bruno also knows since whenever he comes to pick up Martin he "always wore a white smock and a tartan apron, as if he just stepped out of his kitchen."

Because Bruno only knows superficial details about his friends and nothing outside his little world, he is entirely innocent; in fact, he does not even know what his military father does other than that he is "a man to watch" and the "Fury has big things in mind for him"--words he must repeat when asked by the other boys what his father does. His mother, too, reiterates that his father's job is "very important," and says little more. 

How are innocence and wisdom explored in Boyne's The Boy in the Striped Pajamas?

In short, innocence and wisdom are explored through the character of Bruno in The Boy in the Striped Pajamas.  Bruno's innocence often proves his wisdom. Bruno is innocent of the philosophical evils and the physical evils behind the Nazi regime.  Due to this innocence, Bruno questions everything.  It is in this questioning that Bruno exerts his wisdom and finds the truth.  Here is a quotation that is a perfect example:

What exactly was the difference? He wondered to himself. And who decided which people wore the striped pajamas and which people wore the uniforms?

Bruno shows his innocence here in his confusion.  He cannot understand why the Nazi soldiers have placed certain people inside the fence while others remain outside.  The wisdom Bruno imparts here is apparent:  there is not a difference between the two kinds of people (Germans and Jews).  They are all humans and, as such, are worthy of respect.  

How does the author capture Bruno and Shmuel's innocence in The Boy in the Striped Pajamas?

The purity within Shmuel's and Bruno's friendship enhances their innocence.

The Boy in the Striped Pajamas is set in one of the most complex and brutal time periods in human history. The backdrop of the Holocaust and Auschwitz triggers profound questions that relate to evil, goodness, justice, and fairness. However, in developing the friendship between Bruno and Shmuel, Boyne conveys innocence through a disarming simplicity that cuts through these philosophical and moral intricacies.

The start of their friendship is how many children view making friends. Bruno and Shmuel connect because they are the same age and share the same birthday. Kids sometimes feel that these coincidences reflect a permanence to their friendship. It is almost as if both boys feel that they were meant to be friends because of these coincidences. As they get to know one another, they share more similarities that enhance their innocent view of friendship. Bruno is happy when he finds out the Shmuel also had to leave his home and world behind. When they embark on their "final adventure," Bruno remarks on how "extraordinary" it is they look alike with their shaved heads and their striped pajamas. It hits Bruno that "they [are] exactly the same." The similarities they share and the belief that these connections prove how both were meant to be friends communicates innocence.

Another way that Boyne communicates the innocence within Shmuel and Bruno is in how they do not speak in political terms. The reality is that Bruno is the son of a commandant. Shmuel is a prisoner in Auschwitz. This creates a political tension between them, one where the ethics of the aggressor meets that of the prisoner. However, their innocence is enhanced because their friendship transcends the political. When Bruno affirms to Shmuel that they will be "best friends for life" and when he holds his hand in the gas chamber, it is clear that there is an innocence to both of them that goes beyond the affairs of the world. Boyne communicates how purity and innocence can triumph over evil and malevolence in the world.

In the movie The Boy in the Striped Pajamas, how does the opening scene show Bruno's innocence?

The movie version of The Boy In The Striped Pajamas is based on John Boyne's original novel which traces Bruno's short life as he, a German and son of a Nazi Commandant, becomes a victim of Nazi Germany's attempts to annihilate the Jews. John Boyne never intended the book to be factual but was criticized for his inaccuracies and oversights as the book has such a serious historical theme .

At the beginning of the movie, set during World War II (WWII), Bruno is running through the streets with his friends, oblivious to the danger that could lurk around the next corner. As yet, he has no idea that the family will be moving and he will not see his friends again. 

The story is intended to make readers or movie-watchers appreciate that the concept of WW II is so appalling that the horror of it cannot be conceived. Many people in Germany were much like children in their acceptance of Hitler's methods during WW II and, because they never asked questions or dared to defy the regime, they unwittingly became complicit in it. The Boy in the Striped Pajamas, and Bruno's scene with his friends, highlights what can happen if people use their ignorance as their defense. Bruno and his friends, despite appearances to the contrary, remain unaffected by the fact that Berlin is a target for Allied forces. They are unsupervised. This stresses their innocence as they are children, not evil perpetrators of terrible injustice. Bruno is so sheltered that, even when he meets Shmuel, he has no concept of what is taking place. 

Tragically, this will shape his future. Running in the street with his friends reveals Bruno's absolute trust in what his parents stand for and also highlights the misplaced trust of so many who, in reality, allowed Hitler to commit such heinous crimes unchecked by those who are supposed to know better.