To understand why atoms can’t fall through each other—despite the huge amount of empty space in them—we first need to think about electrons. Remember, the nucleus has protons, which are positive. The electrons are negative and attracted to the protons, so they orbit the nucleus.
A hydrogen atom has one proton and one electron. However, remember we also said the physics for electrons were strange. Namely, they are quantum mechanical. What this means is that they are kind of everywhere around the nucleus, without being anywhere exactly. Weird, right?
What this means is they are kind of a blur, or a smear. Think of the space around the nucleus as being a cloud, all kind of negative.