I think every company has a clear reason behind why they picked what they picked. They go for a particular tech over which they've in house expertise in. For example, Zeta in Bangalore, which is a booming startup uses Java for their backend. Let's say someone started their career in Java and been at it for a reasonable amount of years, they're probably going to pick it when they themselves begin a project or a company.
At Shippable, my previous job, we used MongoDB in production for two years and later moved to SQL. A key reason being we had a world class expert in SQL and we did realize that our bug count did come down and innovated faster once we designed our schema right. We didn't design the MongoDB schemas correctly because, we perhaps just started out with it by reading the docs.
At Hashnode, we have people who can do anything with MongoDB, given the experience we have in the team on it and hence, have gone with it.
It really is a matter of what people are used to and what they're comfortable with. So, if you still see Java not being used as much as you would like, it probably means that the number of people who are experienced with Java is on the decline. Let's face it, JavaScript can do anything for you and is a lot easier to pick up than Java (Java I believe has a steep learning curve).