Compiling to native isn't exactly black magic and works just as well.
JVM wastes cycles on things like classes, which is not necessary at all. Going forward, Rust has already proven that you can do things at compile time to guarantee things like memory safety.
Compiling to native on whatever random chip is always a recipe for hassles and random incompatibilities which need work to unravel/fix. Having a spec that chip manufacturers can implement (and that can be trivially tested) and/or a JVM that can be exercised and ported to a chip once and validated removes the vast majority of the integration work.
Does it always make sense? No. But clearly a bunch of folks have found it valuable in many niches.
JVM wastes cycles on things like classes, which is not necessary at all. Going forward, Rust has already proven that you can do things at compile time to guarantee things like memory safety.