Atom is a Greek word (and I am also Greek), and it indeed means indivisible. Chemistry used it for ..."atoms" before we knew about electrons, protons etc, in other words the name was first used back when we thought that they were indivisible and the building block for everything else. Then the name stuck, as often happens.
On the other hand, I can see why it causes confusion now, and not even Greeks use the word with its original meaning. I 'd probably change it, but no biggie.