For Batman, though he sees Superman as a collegue, and even a friend at times, he knows that he's truly the greatest threat to the world should something go wrong.
So, being Batman, he has an aresenal of Kryptonite laced objects ready just in case (depending on which version you're seeing). In most cases, it's usually just small batches, as is it doesn't take much for the Kryptonite to work. In the class Batman: Hush series, Batman uses a Kryptonite ring in a battle with Superman. Even with it though, he notes how his punches almost break his hand cause Superman is so powerful.
Still, better to have it, than to not have it, right?