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The reason Voldemort hated his Muggle father was because his father left his mother to die when she was pregnant.
But, later, Dumbledore discovered that Voldemort's father was actually a victim. Voldemort's mother actually raped him with the help of a love potion (and, that's how she got pregnant).
Did Voldemort know this fact? Or, did he kill his father and continue to hate him out of misconception?
It likely wouldn't have mattered. Psychologically, humans can hold entirely contradictory thoughts about the same subject. A good example, and somewhat analogous in this case, consider white supremacists. On the one hand, they're prone to believing how white Europeans are smarter and better than other people on the planet. But, at the same time, they think that Jews/non-whites secretly control everything and run it behind the scenes with elaborate, highly-sophisticated organizations. When you think about it, seems sort of contradictory to believe those two things, doesn't it?
So it could easily be the same for Voldemort. "My Muggle father left my mother to die." "My Muggle father was weak and fell victim to a simple spell." Simple enough rationalization to justify his hatred and loathing, even if someone looking at it objectively could understand that those two things could also be stated as "My magic-using mother raped an innocent man who left his abuser in disgust when he could."
He probably concluded that his father was "bewitched" or "ensnared" but this is a long way from recognizing his father as a victim. In chapter 17 of Half Blood Prince, Tom Riddle Jr. is questioning his uncle, Morfin Gaunt:
"I thought you was that Muggle," whispered Morfin. "You look mighty like that Muggle."
"What Muggle?" said Riddle sharply. "That Muggle what my sister took a fancy to, that Muggle what lives in the big house over the way." said Morfin.
Tom Riddle seemed to value his mother more than his father, as shown in Chamber of Secrets:
You think I was going to use my filthy Muggle father's name forever? I, in whose veins runs the blood of Salazar Slytherin himself, through my mother's side? I, keep the name of a foul, common Muggle, who abandoned me even before I was born, just because he found out his wife was a witch?
Here he seems to think the only reason his Muggle father left Merope Gaunt is because she was a witch. That was enough for Voldemort to side against Riddle Sr. Furthermore, Voldemort was raised in an era where men were not typically viewed as victims in cases of sexual assault. He appealed to the traditionalists in wizarding society, which further narrows the chances of him recognizing his father's situation.
To recognize his father as a victim goes against Voldemort's character. If he knew Tom Riddle Sr. was taken against his will, it would not have earned him any sympathy.
