Puppy scared to be in crate

Our 15 week old puppy protests constantly when she is placed in her crate. The minute we place her in there she begins to shake uncontrollably as if she's scared/nervous. Then she begins crying and whining and shaking all at the same time. At first we thought she was cold so we lined the crate with a thick terry towel. She still shakes and cries. What do we do? We think that she may think that her crate is punishment. Please help.