This is completely normal. There is a conflict between what you know on a deep level and the false consciousness you are required to uphold, and that you do uphold by completing the work.

The ground truth is that, even though your boss probably isn't a bad or mean person, he too has a boss, who has a boss, and following the chain one almost always finds a vested interest in a corrupt status quo whereby a small set of hereditarily connected rent-seekers who stifle progress and don't care about anything but expanding their own wealth and power.

You can make money by collecting small donations from normal, decent people, but there aren't that many to go around, because the fact is that normal humans have almost no economic freedom. Modulo a rounding error, all money is blood money: it comes either from wealthy people and corporations who have evil intentions, or from governments that might have decent intentions but have been corrupted by evil psychopaths from the private-sector elite.

The fact that rich people are paying us to do something is as strong a signal as there could be that what we're doing is poisoning the world, possibly in a way we don't fully understand. Plus, any time we do something as a subordinate, we know that if we perform too well, we are sending a signal to people who are humiliating us (even if in a superficially professional and kind way) that treating us as subordinates works, and encouraging them to humiliate us even more.

The only reason the system doesn't collapse in an afternoon is that we're indoctrinated into bourgeois false consciousness. But something tells me you knew that already.