Simply collecting all of your Java libraries, frameworks, dependencies, etc and getting them running in your app server can take days. Minor changes like adding a db column can end up touching nearly every layer.
All these costs do have benefits. Java ORMs generate much more efficient queries than ActiveRecord, have more flexible querying, and better fit into existing schemas; JSP engines can render tens of thousands of pages per second; Java app servers are easily clustered; and much more. But most of that isn't something small or medium web apps use, so why pay the price?