Ordinary "if...then" statements don't always imply some kind of relation of causality. And even when they do, it's not always the same kind of causal relation. For example:
If you don't study, you will fail.
If there's smoke, then there's fire.
If n is a prime number, then it isn't divisible by any numbers between 1 and and itself.
In (1), presumably the not-studying causes the failing.
In (2), the smoke doesn't cause the fire - rather, the fire causes the smoke.
In (3), it's not even clear what sort of 'causal' relationship we would want to attribute to abstract things like numbers. Does n being prime cause n to not be divisible by any number between 1 and itself? Or does the causation go the other way? Or maybe there's no "causal" relationship at all and it's simply a matter of definition.
So we wouldn't want to define "If A then B" to always require that A causes B, nor would we want it to always require that B causes A, nor would we want it to always require that there's some causal relationship between the two.
At this point you might think, "Well maybe this shows that there are a bunch of different kinds of if-then relationships, so we shouldn't try to translate them all with a single symbol anyway!"
Perhaps. But despite the differences between 1-3, there are common patterns of reasoning that we apply to all of them. For example, the following pattern of argument is acceptable for all three examples above:
Similarly, here's a pretty natural way of arguing for a conditional claim "If A then B": suppose A is the case and then show that B has to follow.
It's no coincidence that these two patterns of argument are exactly the conditional introduction and conditional elimination rules you are probably learning for natural deduction. Once you have these rules, it's pretty easy to show that "If A then B" is equivalent to "Not A or B." So the natural deduction rules are not necessarily based on the seemingly odd truth-table for material implication. Rather, you can get the truth-table for material implication from the "natural" ways we argue with conditionals.