No person has ever looked inside an atom: How do we know that atoms are made of?
Entire books have been dedicated to this question. Here is a brief comment...
Many scientists have contributed to our knowledge of atomic structure. In some cases, their discoveries have come as a result of brilliant experiments whose results have made clear what must be interior to an atom. Examples include the work of J. J. Thomson and Ernest Rutherford in discovering the electron and the nucleus, respectively.
In other cases, advances have been made as a result of trying to get the atom to "behave" in accordance to previously known experimental results, such as the hydrogen line spectrum in the case of Bohr's work which led to the first quantum atom.
Whatever the case, the discoveries made were of the type that said "Here is a logical explanation to my findings. The atom must be like this... If this is not true, then there is no other simple way to account for what we have just discovered."
Does this mean we know for certain that the atom is that way? No, but this means of providing clear explanations to facts about nature, even if these explanations defy "common sense" demonstrates the way in which science works.