You could probably consider tariffs on the open market at a player colony as being additional expenses for creating the right business environment that lets the submarket exist in the first place.
Also, since you own 100% of a company, say factory, why do you still have to pay for produce?
The tooltip for the "Resource Stockpiles" submarket actually explains this! Conceptually, these resources aren't just sitting there; if not picked up by you, they would be used by the colony - either to be sold as exports, or to fill demand, and so on. So you're not paying for the resources, but rather to mitigate the impact taking these resources out has on the colony's economy.
Gameplay-wise, in both cases, these are necessary. If selling on your own market is always more profitable, you'd feel forced to run around more than usual just to sell for a bit more at times. And if you could take resources from your colonies for free, you'd feel like you had to keep doing that and selling them to make a profit, or miss out on it.
(One could mod the tariffs out easily, btw - edit player.faction and add "tariffFraction":0, somewhere. The Open Market iirc uses the market's faction for tariffs, not the submarket's. Not 100% sure if this would apply to an existing colony or only to newly founded ones, though.)