(1) If Superman were in the Matrix, his superpowers would mean very little because they are no longer in the real world. Remember when Neo and Morpheus are sparring in the 1st movie, and Morpheus says, "Do you believe that my being stronger or faster has anything to do with my muscles in this place? Do you think that's air you're breathing now?" Superman's powers would be limited to what he believes he can do. Neo, who has freed his mind and understands that he can do anything, would be able to out perform Superman. Neo's powers would be infinite, and Superman's powers would be finite. Neo 1, Superman 0.
(2) Superman, although powerful in physical ways (like strength, laser eyes, freeze breath, etc), has never shown any super intelligence. Lex Luthor has always been the diabolical genius that Superman thwarts with physical prowess - the noble jock giving a wedgie to evil nerd. Prior to his "awakening", Neo was a serious shut-in style computer nerd. He was extremely smart in the algorithmic thought which works well with computers. Once in Matrix, brain-power rules. Neo 2, Superman 0.
(3) If Neo can fight off several hundred rogue agent Smiths (who would be able to take over Superman's body), he should be able to take on one Superman. I mean, Superman vs 1 agent Smith might be a good fight, put 100 Smiths would be able to take Superman. Neo 3, Superman 0.
(4) Lastly, if Neo and gang can load anything into the matrix (like guns and clothes), then they would certainly be able to synthesize a whole mess of kryptonite, or kryptonite bullets into a chain gun. It doesn't have to be real, Superman would believe it and his body would make it real. Remember the jump program? No one makes the first jump - even though superman can fly, it means that his initial disbelief is impossible to overcome. Therefore, having experienced the detrimental effects of kryptonite before, would have no choice but to believe it was real. Neo 4, Superman 0.