AC circuit theory and quantum mechanics require the use of complex numbers -- that is, the square root of negative one. In a very real sense, taking the square root of negative one sounds incredibly stupid. In fact, imaginary numbers were a very divisive issue when introduced (not unlike negative numbers before them). What does it really mean to use i? What does i map to in the real world? We're trying to calculate voltages here.. does it make any sense?
Well, probably not. I could start talking about how i sort of extends the number line in the second dimension, and so forth, but that would only move the goal post (what about hypercomplex units j or k or l ... ? ). So that's why the best way to see sqrt(-1) = i is as a rule.
Second of all, material implication is also a rule. There's nothing to connect to the real world. The problem with logic students is that they often don't understand the differences between abductive, deductive, and inductive logic.
You mention atheism vs. religion (I assume you mean theism vs. atheism, as you can presumably have some kind of religion without a deity). When trying to win this kind of debate, you first need to pinpoint what kind of argument you're dealing with. If, for example, you're dealing with an inductive argument, the rules of deduction will not hold -- especially a rule like material implication[1]. I think that your problem is trying to apply formalisms built for one kind of game to another kind of game. Natural language is not logic. Just how Chess is not Checkers.
Going back to material implication for a second, what really made material implication "click" for me was studying the Deduction Theorem[2]. This is, of course, a bit more advanced, but understanding MI from a "provability" perspective really clarifies why it's so obviously true.
[1] http://ac.els-cdn.com/0888613X94900027/1-s2.0-0888613X949000...