Java has much, much, much, ..., much better multi-core support than C++. Seriously. To do multi-core processing in C++ you would have to download, install and learn an entirely new library, with all the lack of trouble-shooting help that implies. Alternatively you could code it from scratch. Even then you have to write custom memory management code to prevent the thousands of possible bugs that can occur, and, unless you spend hundreds of thousands of man-hours perfecting this, it will be far inferior to Java's native garbage collection (which is automatically threaded, fyi). C# is the only c-like language comparable to Java for multi-threading.
It's easily possible that Notch hasn't implemented threading effectively in Minecraft so far. It's likely that he will do so before the game leaves beta. Multi-threading introduces huge potential for bugs, so postponing it until the game is in feature lock and reasonably stable is a good option (the other good option being designing it to support multi-threading from the ground up, something Notch probably wasn't thinking about when his entire userbase was himself). This will most likely be part of an overall optimisation push.
That said, Minecraft will have a lot of options for threading. The lighting code can run in its own thread, as can the graphics calls themselves. File IO can probably go in its own thread as well, as long as protection is put in place to prevent access of a partially-built chunk (either deferring or waiting). Monster AI can probably also go in its own thread, and the same with non-water/lava physics.