It's Bethesda's "owners" ZeniMax (the companies consist of the same people). The really bizarre part of it all is that they've explicitly praised DoomRL as a fan project in the past.
It's not impossible that the legal department is going rogue on this one, and it wouldn't be the first time that kind of thing has happened, which would probably result in this blowing over soon.
More likely, it has something to do with Jupiter Hell's kickstarter, and more importantly John Carmack's endorsement of it. It is entirely possible this is an attempt at gaining (further) revenge on him instead of anything to do with DoomRL.
On the bright side, Jupiter Hell's kickstarter is likely to go viral tomorrow with how much the gaming media have picked up on this story. Even gaming journalism isn't evil all the time.
Yeah, Jupiter Hell really couldn't ask for a better marketing boost. That delicious Streisand effect.
Especially since just about everyone is saying this is about the kickstarter. If it is, that's ridiculously petty, and all the more reason to get out the pitchforks.
These things are often driven by a legal department that lives in a completely separate world from the content part of the company, but unfortunately there's no way to punish those separately. And there must be punishment.
Yeah, these things happen all the time, all across every media industry. But this is a special case. Normally, it's just shutting down some overzealous fans of a property that has little precedent for fan-made content, and they try to do things like direct remakes of old games. Still kinda shitty, but not in a way that's especially ironic or harmful to the whole fan community. Here we have a case where this legal action immediately follows the successful revival of a long-dead franchise, and that revival is directly, explicitly built on decades of fan-made content. Would not have been possible without it. I just can't get over how shitty that is.