I'm of the opinion that copyright and IP laws when it comes to fantasy and science fiction properties are a huge joke, and demonstrate how the entire system needs to be worked on.
To be honest though I do not know enough about Minecraft (despite having a lifetime "subscription" from having donated fairly early on... or I should) to comment as I haven't really played it. There could be more to this than the simple usage of the name, and it could have to do with some of the content Notch/Mojang is choosing to include.
One also has to remember that copyrights need to be defended, if you knowingly let certain things go for not being "close enough" to an infrigement, when a serious infringement comes along the people responsible can then point at the other groups that were knowingly allowed to do these other things. If you don't enforce a trademark you can effectively undermine and lose it.
From what I've seen of Minecraft it's pretty much a giant sandbox, where you play largely from a first person perspective with the guy's hands showing, and most of the combat taking place with melee weapons and such. You also do crafting, can move items around, and tons of other stuff.
Just from what I've seen of the game it does bear a lot of similarities to "The Elder Scrolls" series. Now, Bethesda did not invent that type of game, and they aren't attacking it on those grounds. What they probably object to is a game that has so many similarities to their product, with a name that is also very similar and could lead to confusion.
To most of us game nerds we are aware of "Minecraft", and even if we don't play it can point to all the differances. To a more casual player who is only familiar with a big product like "The Elder Scrolls", looking at a screen shot of Minecraft guy's hands with a sword and shield fighting an exploding pig or whatever, and the title "Scrolls", it would be pretty easy for them to assume some connection despite the differances in graphical quality.
If Bethesda lets this go, someone else could say make a game called "The Old Scrolls" and directly crib off of their product, and then someone could point to Mojang and say "well they did it, so we have precedent".
The point here is that the situation is messed up, but I don't think that this is the same kind of trolling we saw with the word "Edge". The way the system works, Bethesda is kind of in a position where they have to be concerned about precedent, whether we as fans like it or not, and the superficial similarities are pretty obvious, and to someone who wasn't really all that knowlegable about games, they might be lead to the impression that there is a connection.
We also don't know all the details here either, there might have been communication between Bethesda and Notch we're not hearing about, before things went in this direction.
I also notice Notch seems to be trying to rally fans, more than anything at this point. While I've been wrong in the past, what little I know about this area of law makes me think he's going to lose badly if it goes to court.
Of course then again while I thought the movies (especially the first one) were decent, I kind of feel that "Underworld" violated White Wolf's properties. Not just because of the Vampire Vs. Werewolf thing, but the simple fact that they ripped a lot of the first movie off almost verbatim from a story called "For Love Of Monsters" that White Wolf had the rights to and was set in their universe... and understand something, I generally loathe White Wolf for reasons I won't go into, I just happen to think they were right there, and I called that one wrong. While most fanboys were going on about the whole "White Wolf didn't invent Vampires and Werewolves" and showing stylistically similar things, I think people tended to overlook the point about that paticular story and I thought that was why they deserved to win, my personal feelings aside.... the point here being that while I'm frequently right in these cases, I've been wrong in the past.... and Copyright Laws for this kind of thing are a huge mess to begin with and actually lead to battles over precedent that shouldn't ne nessicary. People have to go to court over copyrights when they might otherwise ignore the issue if it wasn't for the way the system works.