The audience makes assumptions that Leonard was tricked and wronged by Teddy in the beginning of the movie because of the semi-friendly relationship that they have and that Leonard finally got his revenge. The audience's assumptions coupled with the nobility of Leonard's quest, avenging his wife's rape and murder, clouds the judgment of the audience and they let feel only sympathy for Leonard Shelby. Instead of thinking of Leonard as a murderous fiend, the audience thinks of him as something of a wounded animal. "Poor Leonard, he is avenging his wife's murder while dealing with such a terrible condition." This is no doubt the sentiment of the viewer throughout most of the film. It is only at the end, or at the beginning in this case, that the audience knows the true nature of Leonard Shelby. He is determined and perseverant in his quest for vengeance, but he does a very bad ting in the beginning. Leonard's decision to set himself up to kill Teddy out of anger for stripping away his sense of purpose makes him a villain. This plot twist is what makes the audience realize that they have been manipulated. There really are no protagonists in this film, not even Leonard Shelby.
For the first few minutes of Memento, one feels sympathy for Teddy. Why was he shot? Did he deserve to have a bullet put through his head? With such a messy, bloody death, who could help but feel sorry for the guy. Of course, minutes later, the audience sees Leonard's notes to himself scribbled on a Polaroid photo of Teddy. Leonard tells himself not to trust Teddy and that he is the one he is searching for. From this point on, the audience believes that Teddy is no good, and they do not trust him, just as Leonard doesn't. This is another example of Christopher Nolan manipulating the audience to jump to conclusions. The audience knows practically nothing about Teddy or what he wants, yet assumes he is Leonard's enemy.