My opinion. It's partly because teams who do webapps tend to be small, young and agile. First, prejudices: they prefer new things (Java is old); they dislike the environment that is Java's home (big enterprise) and the practices and personalities types that go with it (perfectionistic, professional, conservative).

Second, real reasons: Java is verbose and statically typed, and therefore it takes more work to make changes - it is slower to develop in and less flexible/agile. These things really count when you want to try out an idea; and when you need to adapt it. There's also a community effect, where all those early adopters are working with Ruby/Python, that's the platform cool stuff gets developed for (eg. sinatra, github, haml).

Technically, it's possible to write a sinatra in Java (I have; using annotations for urls); but who would use it? I actually love Java myself, including its static typing, and use it in my startup. But when I've played with Ruby - even as a novice without knowing the tricks - I found it much quicker to develop in, and the code easier to understand because less cluttered. It's probably not as reliable; and the code doesn't run as fast; but these things just don't matter for prototypes and early versions.