What is the theme of Thomas Harris's Silence of the Lambs?

The theme of The Silence of the Lambs is certainly about evil, but it is more nuanced than that. The most prominent theme that spreads throughout the work is the idea of betrayal and trust.
In the novel, there are two primary evil characters, Hannibal Lecter and Buffalo Bill. Both of them work within a trusted structure, betraying that trust at the final hour to make their evil action. Bill speaks with and seduces women, before kidnapping and eventually murdering them—certainly evil and sadistic, but also an act of betrayal.
The climax of the story is the ultimate betrayal. Lecter, who has worked to gain the trust and confidence of Clarice, the protagonist, uses the deal they strike after he helps her find Buffalo Bill to escape. Being a prolific serial killer and cannibal, he performs cruel and torturous acts to gain his ultimate freedom, following the same pattern as Buffalo Bill—sadistic, evil, but more importantly, a betrayer.

The main theme in Thomas Harris's Silence of the Lambs is the nature of evil and the many ways that evil can be acted out. For Clarice Starling, the protagonist of the book, evil is a force that she sees every day in her job as an FBI agent. While investigating the grotesque crimes of the serial killer Buffalo Bill, Starling has to work through the evils of her own life and the evils of serial killer Dr. Hannibal Lecter, her informant.
Unlike the other FBI agents in the novel, Clarice Starling sees the actions of the serial killer through the eyes of the victims. This is a distinct difference that provides her with empathy in direct opposition to evil. Starling's empathy does work to give Dr. Hannibal Lecter, the prime figure of evil as a force of nature, moments of sympathy. In their transactions, Starling and Lecter alter from a balanced relationship of civility to a harshly tenuous working relationship that shows the dichotomy of the innocence versus evil they embody.
Buffalo Bill and Lecter are directly evil despite their differences regarding their civility, but Harris points out that evil can be subtle and less transparent. Lecter makes this point to Starling, stating that evil is not always apparent. Evil can take the form of selfishness (like Jack Crawford) or greed (like Dr. Chilton).