She believes him because he is protecting her as much he can. Because he came down to help her. Because his story about Snape's memories has the ring of truth to it. Because the stark misery on his sharp features isn't something she thinks can be faked. So Hermione believes Malfoy, and tells herself that she is...lucky, relatively speaking. After all, it would be so, so much worse if Malfoy hadn't hidden her away from Voldemort's notice. She may have been humiliated, violated, and hurt, but all of those things would seem like comforts if she'd been tossed to Voldemort, she is sure. Hermione tries very hard to focus on the positive.