The thing loads of people forget is that if you don't try to protect your trademark, you lose it. One of my previous employers went through exactly this scenario, where AT&T tried to argue that they hadn't tried to protect the use of this company's trademark, and therefore had lost it. It was certainly eye-opening to hear that story. Anyway, it may be that they even like what the DoomRL dev is doing... But if they don't send a C&D letter, they risk losing their trademark on the name "Doom".
Can Bethesda issue a revocable license to DoomRL for the use of "Doom" and still have their trademark protected? Since it doesn't seem like Bethesda cares whether or not DoomRL exists, and since it would provide good will and good PR towards Doom, this seems like a better move than sending a C&D, which just causes hostility.
Sure, but then you're on the hook for what they officially do with the name, since you've sanctioned them.
Then you come to the cost of doing this while protecting yourself. Getting lawyers to draft up something appropriately restrictive is probably expensive, and still unlikely to cover all the problems you might run into, and getting the project to sign it might be hard since it's in their best interest to have a lawyer review it to make sure it doesn't give away IP, and that costs money...
The author endorses racist/sexist views, comes out for child labor, and incorporates those themes into their work, or somehow publicizes that fact in relation to your property. The details don't matter to 99% of the people out there, if an official Doom product endorsed racism, Bethesda would definitely be dealing with the fallout.
I'm not sure how likely it is factors all that much. When you have a hundred million to billion dollar business, why risk allowing anything even remotely like that which might harm your brand? It's much easier to just say no.
