Thanos "rescued" two children just to train them to be ruthless killers. From a young age, Thanos forced his two daughters to fight each other, inciting cruelty and an unhealthy rivalry between the two. He even replaced Nebula's body with mechanics as they went in order to improve her. What kind of father pits his children against each other? That action alone proves that he is a villain. No father, no matter what, should place that kind of cruelty on his children.
Thanos was simply doing what he had to do. He needed and wanted to raise strong children that would fight and work by his side without fail. He was doing what he needed to do.
[P1] Thanos abused his daughters [P2] This classifies him as a villain