This is not the case, Valve does not take a cut out of generated keys.
The issue is that Valve doesn’t allow developers to mass generate keys for low cost/charity bundle purchases, that’s why if one purchases a game directly they’ll (usually, if a developer has set it up) get a key but not when they purchase it as part of a large bundle.
More specifically, Valve’s terms for generating keys states that a game going on sale elsewhere means that it must also go on sale on Steam; given that massive bundles like the ongoing Ukraine one aren’t feasible to put together on Steam, neither is giving out keys for purchases through said bundles.
There’s two ways Valve could remedy this; they could change key generation terms when charity is involved to allow this use case, or they could provide developers the tools to organise their own charity bundles on Steam. It’s unlikely either will happen though unless a significantly large portion of the community makes a fuss about it. Feature requests like this can be done on Steam’s built in community forum, or possibly on their subreddit.