How many times have you tried to put clothes on him? Maybe he just isn't used to wearing them yet. My Stedman LOVES wearing his clothes - he actually prefers to have something on his body, lol. The only thing he will NOT tolerate is anything on his head, or in his hair...but he LOVES his clothes!
Maybe once your baby gets used to them he will be fine...but I do agree with everyone else, if he is TOTALLY uncomfortable wearing them, then I say just let him be naked and free!