It's the collective we, not you and me. You can substitute other theories like the sun revolving around the earth if flat-earth is bogging you down. The point is if we assume theories are fact we turn our minds off. Thinking should never be limited or based on assumptions of certitude. Assuming theories are facts is like howling at the moon - it might make you feel a little better but it does not accomplish much. BTW: I am pretty sure that is not really your "logic" - I was just pushing the point to illustrate a concept.
Nonsense. Theories are what make it possible for us to think creatively. And we get nowhere if we're constantly wondering about the truth of our premises. If every time I get a discordant result, I consider the possibility that the atomic theory might not be correct, that perhaps electrons don't really exist, that maybe the Coulomb force law doesn't depend on the inverse second power of distance, etc., how far would I get? The answer is, nowhere.