In nearly every version of the franchise, Flash Thompson idolizes Spider-Man, but he and Peter Parker can't stand each other (at first - in the comics, they grow into good friends).The culprits each separately hate him both as Bruce AND Batman, but it is his Bruce Wayne identity that got him in this mess- Lex Luthor wanted revenge on Wayne since Luthor is now President and Wayne pulled out of his government defence contracts in protest, but he hired the assassin David Cain to do the job, unaware that Cain also had his own grudge both because Cain was one of the mentors Bruce had as a youth, and because the new Batgirl happened to be his daughter Cassandra Cain and he resented that she was working with Batman. In Bruce Wayne: Fugitive, Wayne is framed for the murder of his girlfriends.In both cases it is an incredibly petty motive as they each came from wealthy families who knew the Waynes, and were jealous because the Waynes were a genuinely loving family while their own parents were abusive, so they target Bruce purely out of spite for things he had no control over. The villains Roman Sionis (Black Mask) and Thomas Elliot (Hush) both started out with grudges against Bruce Wayne personally rather than Batman, although the latter only turned to supervillainy after learning that they were the same person.
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When played for drama, the superhero might actually be in genuine danger from a villain who hates them in their civilian guise, but indifferent to the cape, though in such cases overlap will likely occur when they either figure it out or simply get tired of the hero interfering with stuff that is none of their business. Sometimes the subject may not have superpowers, they may just be famous and have fabricated their more well-known persona so that they can live an ordinary average life when not in the public view. Sitcom Archnemesis can also play into this role. Not realizing that the person they are actively victimizing is actually their favorite Superhuman and that there will be karmic payback for what they give out later.
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It is usually a case of an Alpha Bitch or Jerk Jock doing what they do best, being mean to someone just because they don't like them. This is often played for comedy when a Superhuman encounters someone they know in their Secret Identity and reacts according to how that person treats them in their downtime, usually with a Snub.