Ideally you would have portable bytecode that compiles Just In Time to native code. I think the reason bytecode interpreters exist without JIT is due primarily to the practical fact that native code compilation adds complexity to a virtual machine. It takes time to build, debug, and maintain that additional component. Not everyone has the time or resources to make that commitment.
A secondary factor is safety. It's much easier to verify an interpreter won't crash than to guarantee the same for native code.
Third is performance. It can often take more time to generate machine code than to interpret bytecode for small pieces of code that only run once.
