The steps that follow aren't necessary for the Steam Deck. If you're on a Steam Deck, Valve already did this for you. You only need to do this if you're running Linux on a desktop or laptop.

You also don't need to do this if you're just using language mods, since those don't inject any code into the game. It's just necessary for gameplay-affecting mods (Fools, Items, Enemies, UI tweaks, etc.)

If you're using a desktop or laptop with Linux and your gameplay mods aren't loading, here's how to fix it!

Find Brutal Orchestra in your library. Click the gear icon for the game, or just right click the game, and select "Properties"

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In the window that appears, put the following text inside the "Launch Options" box:

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Then, go to the Compatibility tab, and enable the "Force the use of a specific Steam Play compatibility tool" checkbox.
A dropdown box will appear under it, select "Proton Experimental".
This will force Steam to launch the Windows version of Brutal Orchesta through Proton, instead of using Brutal Orchestra's native Linux build (which doesn't appear to load BepInEx, the modloader Brutal Orchestra's Workshop uses.)

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That's it! Your mods should be working now. You might have to enter the Mods menu and re-enable your mods. Enjoy! Or else.