Because there is a mountain of evidence. Especially her own lies. She kept changing her story. First she was at her boyfriend's house, then when they proved that she wasn't, she was at the scene and she accused someone else. But of all the other evidence, explain to me this: How did Amanda know that Meredith was sexually assaulted before anyone else did? If she wasn't part of the crime she couldn't know that?
And how did she and her boyfriend know nothing was stolen before the other roommate came in and checked her stuff?