There are "bare metal" machines based on virtual machines. Most recently, there have been various attempts at a Java Processor which would run a JVM (well, JM since its not virtual) in hardware. They do exist - though not in general purpose machines that we use, they more harken back to the original embedded idea that Java was born from.
This harkens back to the Lisp machine which approached CPU design instead with high level instructions in the CPU itself.
The reason is... you don't really get that much out of the specialization at a hardware level... and the direction of research has been for smaller instruction sets with multiple cores rather than trying to make complex instructions. That's where the money has been chased and thats why people are exploring that path more.
The question to consider - is narrowing down your available programs that the system can run worth the investment cost of creating such a system. Furthermore, as the general purpose processors get faster, can you keep up with a viable alternative?
... cheaper desktop PCs soon were able to run Lisp programs even faster than Lisp machines, without the use of special purpose hardware. Their high profit margin hardware business eliminated, most Lisp Machine manufacturers went out of business by the early 90s ...
From Wikipedia on the Lisp Machine.
Note that last section on the other language-optimized computers which includes the above mentioned Java Processors. They just haven't been commercially viable in most situations (and none of them for a general purpose machine).