Space is expanding, not matter.
The space between galaxies, and the space between molecules are both expanding equally.
There is a lot more space between galaxies, so it expands a lot more (because there is more space to expand). The space between atoms and molecules is so small, that the rate of expansion is so slow that the molecules pull themselves back together.
At the current rate of expansion, everything in our local galaxy cluster is still being held together gravitationally, but even if it were much faster it would take a lot to start ripping apart the Earth, much less our own galaxy.
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