For startups, it just seems very poorly suited for the task. I think most of us would agree that the main advantage any startup has is speed and agility. Java isn't that well suited to rapid development, at least not compared to Python or Ruby. It doesn't offer any potentially game-changing technical advantages over the mainstream like Scala, erlang of JavaScript might. Java is a sturdy, reliable language that is very well suited to fairly boring corporate work. It's just not rock and roll though, is it?
Think about the standard startup rhetoric - do one thing and do it well, start small and iterate rapidly, split the market with something unique. If you're going into battle against an incumbent, you need to change the rules of the game - you don't want an AK47, you want an IED. If you're trying to build disruptive technology, it seems obvious that you'll be better off using tools that are themselves disruptive.