It's the same as making a remix of a song. The base of your new version is still the original authors work, so the author deserves a cut. A mod is akin to a remix of the game, and that remix is still mostly Bethesda assets, not to mention running atop their engine.
The game still has to be paid for to play the mod. Bethesda _already_ got their cut when the user paid for the game before even considering the mod.