Unfortunately, that's not a terribly good example, since it's actually pretty easy to deny the existence of nitrogen in the atmosphere. I've certainly never seen any nitrogen in the atmosphere--and God knows, I've been looking for a while--I've only heard other people make the claim that it's there, and that they have proof. Sure, maybe they think they have proof, but they could be lying, or they could simply be misinterpreting the information, or acting on incomplete information. To accept any of the evidence they offer means first accepting, a priori, the fact that their underlying conclusions aren't flawed, that they're not simply crazy, that they actually know what they're talking about, and that there is in fact actually something meaningful there for them to be talking about. Deny any of those, and all the arguments for the presence of nitrogen in the atmosphere come to naught.
Sure, you could claim that there are other things that are best explained by the presence of nitrogen in the atmosphere, but you can't conclusively prove that those things couldn't have some other cause--you literally can't, since there's no way to prove a negative (that I'm aware of, anyway). "Nitrogen in the atmosphere" could be nothing more than a convenient fiction that we choose to accept because it makes other things make sense.
All of these arguments, conceivably, apply to Batman's position on magic. Sure, he's seen plenty of stuff for which "it's magic!" serves as a working explanation. But to accept that as the true explanation means accepting that there is no better explanation available, and that may simply not be the case. As Bats points out, there could be another explanation for all these phenomena, it just hasn't been discovered yet.
Now, I'm not saying there isn't nitrogen in the atmosphere (honestly, I couldn't care less either way), nor am I saying there's no magic in the DCU. I'm just saying that Batman can easily hold the position he holds without committing any logical fallacy (that I'm aware of). He's just making it harder for himself, since he's denying something that most of the people around him accept as true--but when has Batman ever been the type to go along with what other people say just to make his own life easier?