The $60 pays for the game, but to develop a mod for it, you're using tools they've made for the game. They didn't have to provide those tools, they're an additional service that Bethesda offers. Bethesda also added workshop support in the first place. 45% is outrageous, but a 10% cut would be acceptable and help fund the development of better tools and improvements to the mod community.

Agreed.

The fact that it can be so heavily modded is what drives continued sales long after the initial release.

And the modders are building on the incredibly successful IP of Bethesda, riding on their coattails. Why shouldn't Bethesda get something like a royalty? It happens in pretty much any other kind of IP - music, books, movie merchandise and so forth.

If you're selling something that's largely due to the popularity of the source material, why is the idea of a royalty problematic?

$60 gets the user the game.

Maybe it's appropriate to liken the royalty to Bethesda, to the per-sale royalty agreements that gaming engines have struck with some developers? Skyrim-as-development-platform is not entirely unlike Unreal-as-development-engine.