I wouldnt sweat him hiding away. In fact, later on, you will be happy he feels so comfortable in the crate. It will make things so much easier.</p>
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But as Supra said, get to his level and be patient. I am a bit surprised that he would not have scurried around your pad a bit, but with a shelter dog, you dont always know exactly what the dog's past is. If it continues for a few days, I would close the crate door for some time so he cant go it and prevent some other hiding places like behind couch and under bed, then open it back up if he gets way nervous. I wouldnt push it too much at first, but I am sure he will come around.</p>