Because it is just one tool in your toolbelt

The Artificer is also a 1/3 caster, like the Arcane Trickster, and many of their spells require an action to use. Therefore, using Thunder Monger every round rules out spellcasting for that round.

At higher levels, the Artificer gains other abilities that consume their action: Blast Wave, Piercing Round, and Exploding Round. This competes with Thunder Monger as they all consume the Artificer's action.

Finally, there are a lot of other default actions aside from Thunder Monger: Ready, Dash, Disengage, Help, etc. When it's more important to run away, Dash or Disengage will help the Artificer more than Thunder Monger will.

Thunder Monger vs Attack action

You may be specifically asking "why use the Attack action over Thunder Monger?" Well, consider that this is like asking "why not use Sneak Attack every round?" The answer is: you should always use Thunder Monger at the level you gain it, if your choice is either the Attack action or Thunder Monger.

The Artificer is not a full spellcasting class, so it needs some way to contribute damage. Just like the Rogue Arcane Trickster, this subclass of the Artificer uses extra d6's on a hit to catch up with the Extra Attack from the other classes. Notice how similar the progression is between this feature and that of the Rogue's Sneak Attack. This shows that the extra scaling damage is balanced, as another class already uses a similar mechanic.

It is also worth noting, if you multiclass and gain the Extra Attack feature elsewhere, Thunder Monger and Extra Attack will clash. At higher levels, Thunder Monger might deal more damage, but Extra Attack will be the winner in terms of damage at lower levels, assuming a high enough Dexterity modifier.

Simple answer from someone currently playing one....

After looking at all the revisions for this class/subclass, I like the thundermonger ability. The down side to it is thunder is loud. Every enemy within earshot knows you are there after the first shot. That is why the silencer is one of the best mods in gunsmith. However, I believe they are not compatable. So, the option is stealth or try to intimidate an enemy who may try to surround your long range backup.

To clarify my stance: In 1 on 1 encounters or equal group encounters, go for the extra damage. When you are outnumbered, go for the discreet kill and make whoever is left search for you while you pick them off.

Also, you should note that the newest revisions allow for up to 4 barrels after all your equipment upgrades...