Every description of a scientific idea always carries the implied disclaimer that we are talking about the present state of our knowledge. Every "fact" is in fact a belief that's held on a tentative basis pending the introduction of better evidence. That sounds quite noncommittal, but in fact it's the best that we can hope for.

One interesting thing about protons is that you can describe the effect of exchanging any two of them in precise terms, and end up with macroscopic predictions that can be tested. So you're not limited to just trying to measure every proton in a bag to see if they're all the same. There are other ways to test the hypothesis.