There's a system set up that protects people profiting off of your work or tainting your brand image. If you spend bucketfulls of cash developing and promoting a video game, someone else isn't allowed to come along, slap the same or very similar name on their inferior product, and leach sales off of you while making your product look bad. I don't see how that's a bad thing.
It's protecting producers and consumers alike. You know that when you go to the store and buy something, it's actually what you think you're getting. The producers know no one else is profiting off of their advertising or established good will, and no one is tainting the image of their company. Who is losing, other than people trying to rip off consumers to make a quick buck?
Hypothetical:
Mojang makes Scrolls and Bethesda says, "no, that's cool." Then ID makes a game called Ancient Scrolls, and Bethesda says, "that's kind of pushing it, but okay." Then EA makes a game called Eldest Scrolls, and Bethesda says, "nope, not cool, suing!" Obviously (I think) EA is infringing on Bethesda's name. However, what happens when they get to court and the judge wants to know why Bethesda is suing EA for their obvious infringement, but not suing ID for their, he believes, obvious infringement? It looks to him like Bethesda isn't actually interested in preserving their name. It looks like Bethesda just has a beef with EA.
By suing Mojang, Bethesda is establishing a precedent. Bethesda is showing, in court, that it has a vested in the name it owns. It doesn't matter that the courts didn't agree with them. What's important is that the legal system decided that the name wasn't an infringement, Bethesda didn't decide it wasn't an infringement.