Man, this is disappointing. It's particularly surprising that Valve has sent a DMCA here, given their history of pretty much all their popular games originating from the modding community or prior art and the history of fan projects like Black Mesa getting somewhat favourable coverage in the Steam store. I wonder if they took issue with s&box coming from Facepunch, which might be something that is eventually profited…
On the other hand when I clicked the Tweet linked in the article (https://twitter.com/TeamFortressS2/status/174515781256337864...) I thought I was looking at an official TF2 account for a while. So I'm not surprised that they are at least upset with some trademark issues.