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It comes down to levels of assurance. The rules of inference you are using are part of your design space. Mathematics at its core is about clever problem solving. When you encounter a problem you have to decide what you would accept as a proof, and this forces you to accept certain reasoning principles.

The caveat is that this is non-trivial and it's very easy to make people accept assumptions which are completely wrong. That's really the main reason to accept the axioms of set theory: People have been trying to poke holes in them for a hundred years and nobody has managed it yet. If you can use set theory (or something equiconsistent) to solve your problem, chances are that nobody will be able to call you out on a mistake.