It's a game, not real life. Any game racism is not bad like it would be in real life. Further, such "racism" is expected and proper in a medieval setting like D&D campaigns are set in. They are not "enlightened" modern societies.
That's fine if you're able to provide a perfectly bright line between what happens in the fiction -- what the characters are experiencing -- and what happens at the table -- what the players are experiencing. Considering that many players, for better or worse, invest a fair amount of their own personality in their characters, for those players, what happens to their characters also, in effect, happens to them as players.
Even more to the point, given that this edition of D&D is intentionally more inclusive of traditional minorities than other editions, there's an increased opportunity that players will encounter NPCs that share some of their own ethnic or other traits -- transgender players will find that their characters encounter transgender NPCs, for example. The inclusiveness thread also notes other examples where players have been pleased to discover NPCs that 'represent' them in-game, and how that representation makes them feel more welcome at the table. Except now, you're arguing that, because the setting is intended to be 'medieval' and not 'enlightened', it's actually OK to show those NPCs being discriminated against or worse, because that's history for you!
Bottom line -- WotC has presented the Forgotten Realms as an enlightened fantasy society. The Realms are arguably more enlightened than our own society in many ways; for example, the weird-looking dragonborn generally don't get much of any negative repercussions for their appearance. Even player character tieflings and drow, descendants of traditional enemies of the 'enlightened' races, don't encounter much in the way of overt racism as PCs -- those races are judged on their actions, and villainous tieflings and drow (as with villainous humans) are judged as villains for what they do, not what they are.
tl;dr - it's a game, but people play that game in real life. You wouldn't use history to justify ridiculous high taxes, so don't use it to justify making other players at your table feel uncomfortable.
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Pauper