My rat is shy and wont come out, he hates being handled and i am becoming a bit scared of him in return.?

I love my rats one of them is great but the other one isn't they havent ever bitten me either of them but last time i took him out he ran away! I dont want to leave hm 9in the the rest of his life, the only time he comes out is when we have to clean hime but even then he is petrified! I feel really bad!