There's a lot of discrimination going on in Lady Esther wants one of their eggs so she can prove it. And just about everyone hates goblins.
But still, there's one playable race in Baldur's Gate 3 that always seems to get the short end of the stick. In of sheer numbers of NPCs who resent them, they lead the pack. While outright hatred is unjustifiable, there are cultural, historical, and political reasons that shape many characters' opinions of this much-maligned race. And while most NPCs' distrust in them is misplaced, there are perfectly good reasons for those of a certain social station to be afraid.

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Everybody Hates Drow In Baldur's Gate 3
Everyone seems to hate drow in Baldur's Gate 3. Drow are technically a subrace of elves, and are roughly equivalent to what other fantasy media often calls dark elves. They have a sunlight-sensitive trait in Dungeons & Dragons that gives them disadvantage on attack rolls, along with natural bonuses to dexterity and charisma. Baldur's Gate 3 changes the game by removing those features, but the lore is intact: most drow still live in the Underdark.
In earlier editions of DnD, races had inherent moral alignments, and drow were always depicted as inherently evil. As later editions have moved away from that kind of generalization, drow have changed, too. There have been more positive depictions of them in DnD and related material, most notably Drizzt Do'Urden, the kind and noble drow hero featured in a series of tie-in novels by R. A. Salvatore. Drizzt himself isn't present in Baldur's Gate 3, although the footprints of his legacy can be seen in an Act Three Easter egg. At Sharess' Caress, Tav can ask a drow escort to roleplay as Drizzt, to which he bemoans, "Not again."
However, NPCs in Baldur's Gate 3 haven't given up their prejudices so easily. Most of the drow portrayed in game are downright devious, and those on the surface still find plenty of reasons to hate drow. They may not be true of all drow, but these are some of the horror stories that might've negatively influenced those NPCs' opinions.
Many Drow Worship An Evil Goddess
Some drow are sworn to serve the deity Lolth. In Forgotten Realms lore, Lolth is the goddess of shadow, chaos, lies, lust, and spiders - in short, not the kind of entity most people want to tangle with. Both Lolth herself and the drow who worship her are known for her cruelty. She revels in torture, violence, and destruction, and compels her followers to do the same.
There are two drow subraces in Baldur's Gate 3: Lolth-sworn drow and Seladrine drow. Once, all drow were forced into Lolth's servitude from birth, but they later split into two factions. This occurred during a schism led by Corellon Larethian, patron god of all elves and Lolth's ex-husband. Seladrine drow follow Corellon's lead, swearing vengeance against the goddess and all who follow her. Lolth-sworn drow still worship the Queen of Spiders, and are marked with intimidating red eyes to set them apart.
However, those who aren't directly involved in the conflict don't seem to understand it. BG3 NPCs who discriminate against drow can't tell the difference between Seladrine drow and Lolth-sworn drow, or at least don't care to. Instead, they assume all drow are evil, masochistic zealots who are willing (and perhaps eager) to kill, steal, and torture to get what they want.
Some Drow Are Of The Absolute's Cult
The main antagonist here is the Absolute, a shadowy force that seeks to replace all life with Illithids by the ending of Baldur's Gate 3. However, the conflict isn't just humanoids against mind flayers. The Absolute has plenty of help from the humanoid side, too, and is worshiped by the Cult of the Absolute as a deity. While plenty of drow still follow Lolth or Corellon Larethian, the party encounters many drow who have converted to the Cult. Likely promised greater authority and parasitic powers, large numbers of drow have turned their backs on Lolth in favor of an Illithid future.
What's more, of the drow cultists the party meets, many of them are authority figures. Minthara leads goblins in attacking the Emerald Grove, since she resents the druids for worshiping a different god. Nere uses his True Soul powers to run a mining operation. Araj sits at Ketheric Thorm's right hand. Although anyone can the Cult - there are humans, goblins, and duergar doing the Absolute's bidding as well - many drow hold positions of rank.
Some Drow Own Slaves
In drow society, slavery is permitted, even normalized. Drow take prisoners during battles and raids, forcing the survivors into hard labor. In Baldur's Gate 3, this is mostly depicted during the party's time at the Grymforge. There, True Soul Nere commands a large group of deep gnome slaves in a dangerous mining operation, so that they might find the mithral Nere needs to reactivate the ancient Adamantine Forge.
This causes many deep gnomes to fear drow, with a reluctance to accept help from them. That fear manifests in game whenever drow player characters interact with deep gnome NPCs. For example, if a drow player character rescues Barkus Wroot from his goblin bullies in the Blighted Village, he assumes that they're going to enslave him.
Still, none of this means that every single drow is evil, or that players shouldn't select a drow character. While some dialogue checks will be more difficult, the game certainly doesn't lock anyone into a strictly evil route. Sure, a Lolth-sworn drow makes sense for an evil playthrough of Baldur's Gate 3, but a Drizzt-like, heroic drow can be a fascinating character in their own right. If the entirety of the Forgotten Realms canon is included, drow are as varied and manifold as any other playable race, no matter how negatively they're portrayed or how ill NPCs think of them in Baldur's Gate 3.