I don't know where you're getting the assumption that Genghis Khan was seen as evil. I think that he is remembered, at least historically, as a conqueror and a barbarian. Though, I'd argue he wasn't a barbarian, but that is an entirely different answer to a different question. Are you referring to the way the Mongol Conquests were recorded in Chinese and Persian sources? Paul Ratchnevsky wrote a very good biography of Genghis Khan. In it he writes:
The magnanimity and generosity of Genghis Khan were widely recognized; it was said of him: 'He dresses his people in his own clothes and allows them to ride his own horses.'
Also:
Favors were distributed without attention to social origin or race. Shepards and stable lads were appointed to command regiments.
And:
Genghis was just as merciless and cruel towards his enemies as he was generous and liberal with his friends and comrades-in-arms. The idea of vengeance was the basis for the nomads' sense of justice; the duty to avenge was handed down from generation to generation. Genghis acknowledged this duty; his life was ordered by the idea of vengeance and he never forgot any insult to himself or to the clan.
With these statements, Ratchnevsky is asserting that Genghis Khan was good to his subjects and cruel to his enemies. I think that can be said for many great rulers, though Genghis Khan might have been more cruel to his enemies than others. He wiped out the Tatars because they kidnapped his wife. An entire population (or most of a population) wiped out because a single group of men stole his wife from him. These are important statements to think about when considering if Genghis Khan is really universally seen as evil.
This might get a little 'Great Man'-y, but bear with me here. Genghis Khan was a great innovator and diplomat. Before he was elected Khan, the Mongol tribes had not been unified in a very long time. The story of his rise to power is fraught with danger and intrigue. He ascended to power with the help of friends he made during his early years. One by one, he and his band of warriors subdued each of the Mongol tribes. The Oirat, the Merkit, the Taichiyut, the Buryat and many others. Along the way, Genghis Khan instituted policies that were, one would hesitate to say revolutionary, but the policies were definitely novel.
Here's a short list:
The Great Yasa
The Great Yasa is the legal code of Genghis Khan. Unfortunately, no copies of it exist today. The information that we have regarding the Great Yasa comes from external sources, the Koko Debter and the Golden History. I should caution that what I've written below the quotation is speculation because the document I'm writing about doesn't exist, so keep that in mind when reading. Leo De Hartog contends that Genghis Khan created the legal code so that he could control the tribes he subdued as stated above. De Hartog writes:
In the Mongol state whatever was laid down in the Yasa had to be followed to the letter. Civil and military disobedience were equivalent to common crime. This resulted in an unusually strong discipline, which in turn determined the life pattern of the Mongols over a long period. The Franciscan monk John Plano Carpini, who visited Mongolia in 1246, was greatly impressed by the discipline. According to him the Mongols showed more submission and obedience than the clergy in Europe. Disputes and differences were always settle amicably.
We believe that several rules were laid down in the Great Yasa. Notably, the Yasa forbade anyone from stealing women from other tribes. This is how Genghis' mother came to be with his father. Yesügei kidnapped Hö'elün from the Unggirat tribe. Also, Genghis' first wife, Börte was kidnapped by Tatars, as referenced above. Wife stealing was something Genghis learned from and forbade between the tribes under his control. Another notable law was the protection of the 'Golden Family'. This meant that the government of the Mongol Empire was set up as an aristocracy, with the Golden Family being the rulers. Essentially, these were the direct relations and close tribal connections of Genghis Khan. This law also mandated that each ruler after Genghis Khan be part of his direct lineage. Additionally, the Great Yasa mandated that if someone of noble lineage were to be put to death, no blood should be spilled. The usual punishment was to be rolled in carpets until suffocated. Several people died this way from the records that are available today. We think that it was a law in the Great Yasa.
Military Organization
Genghis Khan broke with steppe tradition when he ordered his men to take a city, but not plunder until the attack was complete. He also mandated that the treasure was to be divided evenly between everyone. When I say everyone, I mean everyone. If a husband fell in battle, his widow would be 10 times his share of treasure so that they might survive. It would have been kind of like a pension.
In addition to the plunder, Genghis Khan would ultimately decimate an enemy and absorb the remaining people into his empire. This meant that he wouldn't have a problem with that people group again. If you were one of the Merkit tribe and were not killed in the initial attack, you were absorbed into the empire. Your government was destroyed and your countrymen were dead or absorbed with you. Genghis Khan would not have a problem with the Merkits anymore after that. It makes sense in a strategic sense, but it seems cruel...even evil.
He introduced decimal divisions of 10, 1,000, 10,000, etc. In the units, he split up people of the same tribe. There were two reasons for this: 1. He didn't want more than a few people from the same tribe to be together because they might revolt. 2. The Mongols wouldn't lose all of the men from one tribe if they fell in battle The best analogy I've heard for this is WWII. If you sent 40 men from the same small town in Georgia to fight in the same company and that entire company died in a battle, the men from the small town in Georgia would have been wiped out. That kind of distress is hard for a community to handle and it is hard to rebuild. If Genghis Khan split people up, the tribes would be preserved but they would be spread out. Instead of losing an entire population of males from a people group, he might lose several males from several people groups.
Yam
The Yam was like the Pony Express. A general could send a rider with a message across a great distance and the message would usually reach the intended recipient. The Mongols had set checkpoints where a rider could get food, a fresh horse, and water. These checkpoints were spaced between 1 and 3 miles. Steppe ponies could only run for about 2ish miles before they got tired, hence the spacing of the checkpoints. In addition to these outposts, communities always had horses saddled for the messenger of Genghis Khan. This system had not been in place before the empire of Genghis Khan. De Hartog estimates that a Mongol rider could cover between 200 and 300 kilometers a day using this system.
Language
Genghis Khan effectively introduced the written form of Mongolian. The Uigher script was used for the written form of Mongolian. The Great Yasa was written in this form. We believe that all of Genghis' sons and his primary officials were literate but he remained illiterate.
I think your assertion that Genghis Khan is universally seen as evil is incorrect. A better assertion would be that he is recorded to have been both generous with his friends and extremely cruel to his enemies. Asserting that someone is good or evil brings in a moral debate and I don't really think we can argue the morality of a 13th century people based on 21st century principles.
I hope that what I've provided here was helpful!
Sources and Additional Reading:
Genghis Khan: Conqueror of the World by Leo De Hartog
Genghis Khan: His Life and Legacy by Paul Ratchnevsky
The Mongol Art of War by Timothy May
The Secret History of the Mongols by Urgunge Onon (English Translation)
The Mongols by David Morgan
What makes you think that Genghis Khan was evil? I've never seen him as being this way. For a start religious tolerance was commomplace throughtout his empire.