This is probably the best way they could have handled it. It protects the name from abuse while still allowing enough freedom for those wanting to use it legitimately.
Someone registering the trademark underneath them, using the trademark for illegal activities, pretty much anything negative.
Some people seem to be alarmed and think that you won't be able to use node/node.js in your domain names, but you just need to get a license. Like with anything else.
I would prefer that node was part of a non-profit foundation of some kind rather than Joyent, but that is largely under the bridge at this point. It was discussed heavily when this change was made in november 2010:
The thing to keep in mind is that this is just a trademark on a product. It isn't a patent on the idea of a server side evented javascript engine. There is nothing stopping someone from creating another engine that works exactly the same way and that is compatible with all the current modules.
They don't call Ryan Dahl a BDFL for nothing.