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For example, no one has ever seen an atom with their own eyes; it was identified by secondary characteristics.
but we accepted this information as truth without having any proof.

Have you seen it, heard it, smelled it, touched it, tasted it?
I'm not saying it doesn't exist; I'm asking how it was proven to us?!

What kind of heresy is this? {facepalm} Tell me, what is a primary characteristic? Why do we need to see or touch atoms? Why do we need to prove their existence? An atom, like everything that humans give a name to, exists BY DEFINITION. The term was originally conceived to designate an object. If the object in reality does not have exactly the properties initially assumed, this does not affect the existence of the object, in this case the atom.
Let me give an example: it was originally believed that the law of attraction was that all objects except, well, stars and the Sun, are attracted to the Earth (maybe I'm exaggerating, but the point isn't the precise wording, so let's accept it for now). Then clever people figured out that gravitational forces apply to all macroscopic objects. In other words, the law of gravity turned out to be different. And now the question: did we need to see, hear, or smell it to say that it exists? No. We perfectly determined its existence through indirect signs. The law of gravity itself was defined incorrectly, but we knew it existed. The same goes for atoms, microparticles, ourselves, and our planet. All these objects may turn out to be something entirely different from what we think, given the current state of science and the inherent limitations of our thinking. But they definitely exist, no matter what we mean by these terms.