"why not then compile for x86"
Because then you can't take advantage of the specific features of the particular cpu it gets run on. In particular, if we are to read "compile for x86" as "produce native code that can run on a 386 and its descendants", then the resulting code can't rely on even something as old as the mmx instructions.
As such, the end result is that you need to compile for every exact architecture it'll run on (what about those that does not exist yet), and have the installer select which executable to put into place. Or, I hear the intel C++ compiler will produce several versions of the same function, differing only on cpu features used, and pick the right one at run-time based on what the CPU reports as available.
On the other hand, you can view bytecode as a "half-compiled" source, similar to an intermediate format a native compiler will (unless asked) not actually write to disk. The runtime environment can then do the final compilation, knowing exactly what architecture will be used. This is the given reason why some C#/.net code could slightly outperform c++ code on some cpu-intensive tasks in some benchmarks a while ago.
The "final compilation" of bytecode can also make additional optimalization assumptions that are (from a static compilation perspective) distinctly unsafe*, and just recompile if those assumptions are found wrong later.