It's pretty difficult to do language performance comparisons based on a single game. Dwarf fortress, another great indie game involving mining and crafting, is written in C++, has no 3D (it's simply a 2D grid), and uses up a lot of CPU.
That doesn't mean that C++ is slow. It means we have no idea how much these custom indie game engines have been performance tuned, and how much logic is being performed in the background (DF is a hugely deep game). They are both written by a single programmer, not a team of game engine developers.
Edit: I don't doubt that performance tuned C++ is faster than Java. But for a small development team, who aren't building a graphically taxing game, performance optimisation is well down the list of priorities. They are usually better off spending the time expanding their game.
Dwarf Fortress simulates a 3D environment just like Minecraft, though it has much more advanced fluid flows, amongst other things. Most of the CPU use appears to be down to pathfinding, which ends up recalculating a lot when the environment changes.
That doesn't mean that C++ is slow. It means we have no idea how much these custom indie game engines have been performance tuned, and how much logic is being performed in the background (DF is a hugely deep game). They are both written by a single programmer, not a team of game engine developers.
Edit: I don't doubt that performance tuned C++ is faster than Java. But for a small development team, who aren't building a graphically taxing game, performance optimisation is well down the list of priorities. They are usually better off spending the time expanding their game.