I think the reason is more about the shift towards webbased and mobile application then the language itself.
It's about using the tools for the job they were intended for. You're not going to create a windows app in PHP ( even though it's very much possible ) and you're not going to create a web application in Java.
It's not that either language is less suitable, or better, but it's about what they are intended for and what they excel at.
Despite all the hate it receives from the more traditional developers ( Java, C, C++ etc... ) there is no denying that PHP is at the top of the foodchain in that area. NodeJs is moving into that terrain though, and Ruby on rails fills a nice niche, .Net is also very big among enterprise level applications and is the biggest within certain sectors.
Java is barely used these days within that sector ( despite being one of the biggest players in many other sectors like Android ).
What are startups doing these days ? Mostly webbased stuff. One of the current "hip" thing is a combination of a Javascript frontend, several serverside backends ( PHP, NodeJs mostly ) running through stateless microservices, perhaps with mysql, or some other database, or several data layers.
It's all in the cloud, scalable, multi-tennant etc etc... That's what's popular, that's where the money is, so that's where the startups will try to make their start.
Enfin, it's a whole different ecosystem and Java has yet to find it's place there. In my experience ( I started out as a Java dev ), like Bill O'Neil mentioned, within the Java community there exists an unwillingness to look outside of the established methods. There isn't enough going on ( yet! ) within the Java community to "get on the bandwagon" so to speak, and if that doesn't change Java will eventually become obsolete.
I don't think it will come to that, though. Java is still very viable and if a large enough group ( or several smaller groups ) actively work towards expanding the ecosystem ( new frameworks for example ) then we'll see an increase in Java developers in the near future.