I'm going to 'third' the "associate the crate with good things" answer. Feeding the dog in the crate, and staying in the room while the feeding/crate time is happening has helped my dogs in the past. Also, staying calm yourself is important. I know I find it distressing to see one of my pets upset, but getting tense or upset myself just upsets them more. Stay calm and reassuring while the puppy is in the crate, and also when you leave the room.