JDO's popularity

JDO's popularity is growing rapidly because of its simplicity, ease of use, and scalability.
JDO has been deployed in many business critical systems in all primary application areas with great success.
A recent java.net survey showed JDO's popularity.
http://www.java.net/pub/pq/122

JDO compared to other persistence frameworks like Hibernate ,JPA and EJB3

JDO provides a lot of benefits over those APIs. With JDO you can avoid SQL Lock-In because it eliminates your dependence on a particular relational database product.

JDO’s standardized middle layer insulates the application from the underlying SQL implementation(with JDO implementations like the OR mapper JPOX).
And allows to run your application on non relational data stores like OODB (Objects Oriented Databases with JDO implementations like JDOInstruments) , XML stores, etc.
This increases the portability of your application.
If you want to be purely database agnostic, JDO is the right choice.

Performance

JDO provides a caching lifecycle for persistence-capable instances. This reduces memory requirements and increases the performance of your applications.

Development

JDO delivers significant timesavings to the development schedule by eliminating the need for complex custom-written persistence infrastructure.

Finally: JDO is just about objects!