If they weren't used in organized warfare between agricultural states, any answer to "why not" would be speculative. But- why not? Wouldn't a simple carved stick have added power and range to every javelin throw?
Well, a javelin has a metal tip, making it heavier and since you are asking for a speculative answer, I would guess that physics prevent you from using an carved stick together with a javelin since the weight distribution gets skew. The atlatl added range and power to a sharpened wooden stick with comparetively little weight. If you were to do the same with a metal tipped spear I presume you might get the same result as when a catapult is fired without anything to stop the... ehem... decoil? I have no idea what is called, but you know the wooden bar that sits halfway through the 'swing' and prevents the launcher from hitting the ground after firing.
This is of course a highly speculative answer, but OP asked for one as such. Please don't crucify me.
The word atlatl is Nahuatl - Aztec. It comes into English because of the Spanish Contact with the Aztec Empire/Triple Alliance, where atlatls were used regularly in organized warfare throughout the region. The Letters of Cortes mention them, I believe.