My point is that there are some things that are so well-proven that they are fact even if they are called theories. Not regarded as fact because they’re our best guess, but real fact. Germ theory would be one of those.
Pasteurs Germ Theory is that microorganisms cause fermentation. It is an observation, they do cause fermentation. Newton observed that apples fall from trees, apples do fall from trees. Where is the proof of their hypotheses? Repeated observations do not constitute proof. If all you have seen are White swans does that prove that all Swans are white? No it doesn't, all it takes is a single black Swan to prove that theory wrong.
This is how science works. We make guesses (hypotheses) and if they don't get contradicted or falsified they become "theories." Nothing ever gets proven, it just gets refined to the point that we accept it as a given.
Germ Theory, by the way, has been continually revised and refined too. It looks very little like it did a hundred years ago and I expect our version will look very quaint and simplistic a hundred years from now.