I am not sure which Microsoft product you are talking about, but certain Microsoft products are indeed charged this way.

Windows. If Unity is a large part of what makes games work then Windows is arguably an even larger part of what makes most consumer software work. If it's acceptable to charge for Unity usage then it should also be acceptable to charge for Windows usage. After all if you want to install Unity development tools on Windows you need to use Windows. Then following your logic that means Microsoft should be able to charge, in this example charge Unity Technologies, every time someone installs the Unity development tools because the tools literally won't work without Windows.

And if this became the norm then that cost will be offloaded to the customers. That would mean if you've built a new computer and want to play Skyrim you're going to pay x amount to install Chrome (or Firefox), then pay another x amount to install Steam and finally pay another x amount to install Skyrim. That's stupid.

Maybe you tell me which one is the one that does not have any problems and is still simple enough to bill upon?

It's called licensing and Unity developers already pay a licensing fee per year and, in theory, also per user. Some companies reuse keys (not unique to Unity or game dev) between developers because they can get away with it as just the "per user" part is already too hard for licensing companies to properly track and bill.

And to be clear I never said you're stupid. I said your idea is stupid. Smart people can have stupid ideas as well.