Another important reason why scripting languages are more popular is due to the fact that shared hosting environments support them better. Any cheap Linux based hosting plans include PHP/Perl nowadays, but rarely can you find good Java hosting provider with comparative prices. JVMs put much higher burdens on the hosting service providers in terms of hardware resources and human resources.

From the programmer's point of view?

Interesting to see your post here, Ewan. First, I want to thank you for your great contributions to the bioinformatics field, especially your role in the Bioperl project. But secondly, exactly for the same reason, I have to blame you for my current trap in the Perl world nowadays because outside of this narrow bioinformatics field most of the highly paid IT jobs are in Java or C#. Before my last job in Celera, which was 8 years ago, I was a C++/Java programmer and I really didn't like the non-OOP style of the old Perl. But because of the nice OOP structure of BioPerl, I got hooked by it, and currently I spent less time on Java and C++/C# because I have already had a much larger code base in Perl/BioPerl. It's all your fault :)