I worked at a couple of startups that were mostly Java based and had several CLI tools. The focus was building "fat jars" then running them with "java -jar ...", or running scripts that did that. The Java VM was a system dependency and getting it baked into the binary just wasn't a practical concern.
I work at a startup that ships a Java cli to our clients. It is a giant pain in the butt. There are constant support requests from users that are using the wrong version of Java, too old or too new. Sometimes they have to wait weeks for authorization to even install the Java runtime. IT departments are extremely strict about installing Java.