A villain and Antagonist are two very different things. Antagonist is simply someone who apposes the main character - regardless of him being a symbol of good or not - in any way. And it can be any entity or a phenomenon.
Coming to the topic, I don't consider anyone from the list evil. This is a very staunch take on the situation, given that all villages are inherently corrupt. If you call Ataksuki evil, then you should also slap the same label on Mist and Rock villages who used the group for terrorism and killings to expand their power. In the same way, if you call Sasuke, Itachi, Nagato evil, then they are victims of Konoha's endless desire to rein through a sovereign and tyrannical principal without taking any peace treaties or general morals into account. They were willing to do everything to maintain their arbitrary hold; there is no way this is a peace loving village. If you call Orochimaru and Kbbuto evil, then Sand village underhandedly declared a war on Konoha, and killed many. Anyone who thinks that the village are good, is clearly crazy.
- Madara Uchiha was betrayed by his own people. He took the eyes from his brother - who willingly gave it to him - and fought for his clan's honour. And when he lost everything dear to him, his clan cast him aside and signed a peace treaty with the Senju clan. He foresaw that the senju would beray the Uchiha, and he was right. Right after Hashirmam's death, his brother Tobirmama segregated the clan, limited their power to maintain senju hold on the village, and began their surveillance. This was carried over to Hizuren's reign and ultimately became the reason for their demise. Konoha's pro-senju sentiments were the reason behind their death. He wants to lift the veil of peace from the eyes of the world by casting them into another illusion they believe in. A perfect-paradox of perceptions.
- Orochimaru witnessed the transient nature of life through war and became obsessed with the concept of break the cycle of life. Hizuren's decision to deny him the hokage seat pushed him over to the edge, and he felt that life is not only short but is full of betrayals. This solidified his stance on the fickle nature of human beings and that the answer to the truth lies in aligning ones self with more knowledge by breaking the boundaries of life.
- Kabuto was an orphan and his situation was exploited by none other than Konohan skewed, wanton politics that care for no one. The only bond he ever truly formed with someone was the person he was tricked into killing. It was only natural for him to direct his hate back at the people who became the reason for his lack-of-existence again.
- Nagato was yet another victim of Konoha. His village was decimated during the war. He and his little friends - Yahiko and Konan - faced hunger, starvation, victimization at Konhan's hands, and when he tried to achieve peace, Konoha was there yet again to rent his efforts asunder. His reaction was poetic justice; the village that disturbed the peace on a whole, he strove to burn it down so that the rest of the world can live in peace. He even dispatched Hazno who allied with roots division to aid their cause. His end was not fitting at all.
- Sasuke uchiha saw his entire clan slaughtered by the political establishment - I am considering the whole story here, not fragments - and the manipulation of his brother's deep, unparallelled, and compassionate emotions for him. Not only a civil revolt was a horrendous and obviously lame, made-up excuse by the pro-senju lobby to take the Uchiha out of the way once and for all, they didn't even spare the children and people who weren't ninjas at all. Sasuke's reasons are the same as pein's. The village reaped the benefits of their clans inhuman genocide to maintain a tyrannical rein, it's only fitting a paradoxically justifiable to inflict the same level of hate, pain, and loss he - and nagato - went through on the village. If the village is killed, no one is responsible for it, but the establishment themselves.
- Itachi uchiha dearly, and unconditionally loved his brother. As he was expected to be a class A student, a ninja, and a model citizen by his parents, teachers, and peers, he worked for both sides. He didn't want to murder his family because of known known threat factor and on ethical grounds, but Danzo - having a free pass from the governors and elders of Konoha to do whatever he pleased as long as the village prospered - manipulated him by dangling Sasuke in front of him. He presented the possibility that either slaughter your clan and save Sasuke or join them and watch Sasuke get killed in the process.
I want to make this clear to the whole base here, Itachi NEVER murdered the clan to save the village, he did so to PROTECT sasuke and sasuke only. It is made even more clear when Sasuke basically told him that he was going to destroy the village and said farewell, he showed him the full memories and said, "You don't have to forgive me. No matter what you decide to do from now on; I will love you forever". It clearly shows that he doesn't care about anything or the village beyond Sasuke. And that is the high point of his character for me, and the reason he is one of my favourite characters. Family > everything else.
- Zabuza and Haku were the victims of their village's custom's and their policies. Zabuza being a mercenary after slaughtering the competition - which was required of them at that time - took a young boy home to raise him as his equal because he was starving with no one to care for him. He brought him up in his image, and yet, you can tell how he cared for Haku - like a son - and Haku considered him a father figure and was ready to lay down his life for his.
What I want to note here is that you people have a preposterous definition of evil. If for patriotic reasons - which is such a brain-washing tool to galvanize the masses for unjust cause disguised as noble - no matter what a village does, it is good, but if people fight for their family, they are evil? Sasuke and Nagato are evil for konoha, but for people freed from Orochimaru, for people wronged by Orochimaru and konoha, Sasuke is a saviour and for his people Nagato was.
Keep this in mind, there is no such thing as a hero. As one man's or country's hero is another country's murderer. To think that the base is this patriotic is...just plain sick. For me, nothing beats family. Konoha and the rest of the villages be damned. If for their prosperity people like nagato, and uchiha have to suffer, then they deserve every bit of it in return. Pound for pound. This is called, justice in purest and unadulterated form. in short, it is the political system in these countries that is the root cause of evil.