The Rising of the Shield Hero's titular lead faced extreme discrimination during the start of the series. Despite being summoned to a parallel world along with other three heroes, Naofumi Iwatani is the only one who received hateful treatment and was disregarded during important occasions. Viewers are left wondering why the Shield Hero was treated in such a way at first, but this is answered in the latter parts of Season 1.
When the heroes received their retainers, Naofumi was left alone. Princess Malty volunteered to join his party, only to swindle his money and destroy his reputation. Shield Hero deliberately presented Naofumi's character as the worst among the four, giving viewers a bad impression of him. He lacked general knowledge and experiences, and was also uninformed about RPGs. The anime made it seem that, shallow as it is, being the underdog was why the Shield Hero was very unpopular. However, the truth is that a dark force was working behind the scenes.
The Church of the Three Heroes was once the primary religion in Melromarc. As the name suggests, they worship the three heroes -- the Spear, Sword and Bow Heroes -- as gods in human bodies. They preach that they are the people's saviors from the hordes of monsters called Waves, while also believing the Shield Hero is a devil whose primary mission is to destroy the world.
Princess Malty, Naofumi's first betrayer, is a faithful believer. The church's influence extends throughout the entire kingdom, so much so that Pope Balmus easily rallied an army of believers against the heroes. This entity's preaching and vile mudslinging, with huge help from Malty, results in the Shield Hero's poor reputation.
The church also promoted discrimination against demi-humans, leading to the rise of human supremacists. However, the people's hate also has its historical roots. When Queen Mirellia finally made a move and persecuted both her husband and daughter for their crimes against Naofumi, she explained that the king's spite was rooted in a previous war, where he had lost members of his family. The problem was that the Shield Hero fought for the demi-humans, so the king blamed the hero for his loss.
The Church of the Three Heroes also took advantage of the Shield Hero's allegiance and framed both Naofumi and the demi-humans as spawns of evil. As a result, the Shield Hero is worshipped in Siltvelt where most demi-humans reside, but loathed in Melromarc.
When Queen Mirellia helped the heroes, she also took care of the church, imprisoning its leaders and abolishing its beliefs. She even started a new religion based on the four heroes. Although the queen's efforts are noble, it's hard to imagine that the Church of the Three Heroes' influence can be wiped out so easily, especially with how far it extended. If there is indeed residual faith or believers, it may be shown in the upcoming second season of The Rising of the Shield Hero.