Java is slow, most of the heavy lifting is not handled by the GPU. There's still animation, physics, and AI hitting the CPU, all of which are very time-consuming.
Java doesn't exist on consoles, and consoles are a major target for commercial games. If you use Java on PC, you're eliminating your ability to port to consoles within reasonable time and budget.
Many of the more experienced coders in the game industry have been using C and C++ long before Java became popular. The two points above may contribute to this, but I expect that many professional game coders just don't really know Java all that well.
Someone else's point about middleware above was a good one, so I'm adding it to my answer. There's a lot of legacy code and middleware written specifically to link with C/C++, and last I checked Java doesn't have good interoperability. Using Java for most companies would involve throwing out a lot of code, much of which has been paid for in one way or another.
