Here's why:
* Merope was a poor, weak, and neglected witch. She was desperate for love and was under the influence of a love potion she used on Tom Riddle Sr.
* When Merope stopped using the potion, Tom Riddle Sr. immediately left her. He was disgusted by her and rejected her completely.
* Merope, heartbroken and abandoned, died shortly after.
* Tom Riddle Sr. was never found again. His death was ruled as an accident, but suspicion fell on Merope as she was the last person to be with him.
However, it was actually Voldemort (Tom Riddle Jr.) who killed his father. He was conceived through magic and inherited his father's memory. Voldemort murdered Tom Riddle Sr. in a fit of rage after he discovered his parentage and his mother's desperate love for a Muggle.
It's important to remember that the initial accusation against Merope was due to prejudice and misunderstanding. The real perpetrator was Voldemort, hiding in the shadows of his own dark lineage.