Yes, you have to pay the tax whenever you cast your commander from the command zone, whether through Geode Golem or otherwise.
As Geode Golem says, you still have to pay any additional costs. The "commander tax" is an additional cost:
903.8. A player may cast a commander they own from the command zone. A commander cast from the command zone costs ...
One of the rulings for this card on The Gatherer:
If you cast a card “without paying its mana cost,” you can’t choose to cast it for any alternative costs, such as bestow costs. You can, however, pay additional costs. If the card has any mandatory additional costs, such as the commander tax, those must be paid to cast the card.