Well, seeing that their own words aren't enough to convince you I don't expect to do it myself, but just two points:
1) Allocating part of your profit to charity (and getting some not incosiderable tax deductions as a result, by the way) is not the same as being a non-profit organization.
2) Charity aspect notwithstanding, many other online stores offer deals at least as good as those you mention, so I'm not sure what's your point there... Is e.g. Fanatical a non-profit organization too in your opinion?
It's not that I don't believe you, it's that I don't understand this business model. I have no idea who Fanatical is, and the only reason I heard about Humble Bundle is because I backed a Kickstarter project, and the developer/publisher (Red Thread Games) gave me access to the game and its extras (Dreamfall Chapters) on Humble Bundle, and the only reason I heard of GOG is because they also gave me a GOG key for the game. Yes, I'd been living under a rock for the previous six years. I don't understand how there could not be a massive loss, let alone any profit at all, on selling $200 worth of games for $12, even if every game is extremely heavily discounted. Assuming that the publishers and Humble Bundle make enough off of the sale to keep the lights on, how is there any money at all left? The Monthly Bundle surely heavily eats into the would-be profits that would have been made on sales of the individual games if they hadn't been in the bundle.
My understanding of how Fanatical offers low prices is a legal loophole: they buy deeply discounted keys meant for very poor countries, and then turn around and sell them to rich countries.
If you look through their store you will see that most of their games are not really that cheap. Those that are simply are also in most cases already pretty old. Then there are several games that are on sale only for a pretty limited time (which is the same thing GOG does to offer an incentive to buy). There is no need to break regional barrier (like illegal key shops such as G2A are doing) ti make some money with digital keys. It all depends on the publisher and the contracts. Since those keys are all steam keys they even could not sell those keys from poor countries to cheap countries since they are mostly region locked by steam. You might have confused illegal key resellers like G2A, Kinguin ect. with legal ones.