Without a doubt, Shere Khan is a villainous character. He is motivated by his desire for ultimate power over the jungle, and he desires to kill Mowgli at any cost because of his intense hatred for human beings. He is also manipulative, making promises to the young wolves in order to depose Akela, the wolf leader who has been protecting Mowgli from Shere Khan's vengeance since the boy was separated from his human parents. All of this makes Shere Khan a formidable antagonist, a villain in the truest sense of the word.
However, it must be said that Shere Khan is not evil for evil's sake. His background influenced his current mindset. He grew up with a crippled leg, which earned him the mockery of his own mother and others around him. He is known as Lungri, or "the Lame One," and later he becomes obsessed with power, perhaps as a result of being derided for being physically disempowered as a child. His jealousy of humankind's ingenuity might also stem from this psychological childhood hurt. Becoming the most powerful animal in the jungle is perhaps Shere Khan's preferred way of proving those who once derided him wrong. This does not excuse his villainous behavior, but it shows that it does not exist in a vacuum.