The answer is relatively simple, but complicated.
We cannot prove that Peano axioms (PA) is a consistent theory from the axioms of PA. We can prove the consistency from stronger theories, e.g. the Zermelo-Fraenkel (ZF) set theory. Well, we could prove that PA is consistent from PA itself if it was inconsistent to begin with, but that's hardly helpful.
This leads us to a point discussed on this site before. There is a certain point in mathematical research that you stop asking yourself whether foundational theory is consistent, and you just assume that they are.
If you accept ZF as your foundation you can prove that PA is consistent, but you cannot prove that ZF itself is consistent (unless, again, it is inconsistent to begin with); if you want a stronger theory for foundation, (e.g., ZF+Inaccessible cardinal), then you can prove ZF is consistent, but you cannot prove that the stronger theory is consistent (unless... inconsistent bla bla bla).
However what guides us is an informal notion: we have a good idea what are the natural numbers (or what properties sets should have), and we mostly agree that a PA describes the natural numbers well -- and even if we cannot prove it is consistent, we choose to use it as a basis for other work.
Of course, you can ask yourself, why is it not inconsistent? Well, we don't know. We haven't found the inconsistency and the contradiction yet. Some people claim that they found it, from time to time anyway, but they are often wrong and misunderstand subtle point which they intend to exploit in their proof. This works in our favor, so to speak, because it shows that we cannot find the contradiction in a theory: it might actually be consistent after all.
Alas, much like many of the mysteries of life: this one will remain open for us to believe whether what we hear is true or false, whether the theory is consistent or not.
Some reading material:
- How is a system of axioms different from a system of beliefs?