he's talking about a girl that he's done something he shouldn't have with. "let you go to sleep feeling bad as me"=sleeping with someone and they both know they're wrong for doing it. no one else knows whats going on, and its bothering him "i can't get that sound you make out of my head.... no one else seems to be noticing" and he feels bad about himself for it. he's saying that what he's done is mean, that he's a mean person. the phrase "you wouldn't hurt a fly" and "you don't have a mean bone in your body" refer to someone really really nice, who wouldn't do something mean, even as small as hurting a fly. but he would hurt a fly. because he's got a mean bone in his body.
he's talking about a girl that he's done something he shouldn't have with. "let you go to sleep feeling bad as me"=sleeping with someone and they both know they're wrong for doing it. no one else knows whats going on, and its bothering him "i can't get that sound you make out of my head.... no one else seems to be noticing" and he feels bad about himself for it. he's saying that what he's done is mean, that he's a mean person. the phrase "you wouldn't hurt a fly" and "you don't have a mean bone in your body" refer to someone really really nice, who wouldn't do something mean, even as small as hurting a fly. but he would hurt a fly. because he's got a mean bone in his body.