Why most of the people choose Java in IBM FileNet implementation?

FileNet Content Engine (CE), Process Engine 5.X (PE) and Application Engine (AE); all are J2EE applications installed on J2EE Application Servers i.e. IBM WebSphere App Server. (Note PE was a C++ app before FileNet P8 Business Process Manager 5.x)

There are two ways for other applications (FileNet internal as well as external application or custom applications) to communicate to FileNet CE:

EJB transport

The EJB transport is an Enterprise Java Bean (EJB) that runs in the J2EE EJB container of the application server that hosts the Content Engine Service.

The EJB transport can only be accessed through the Content Engine Java API. This is the fastest way of accessing CE.

Content Engine Web Services (CEWS) transport

FileNet CE provides Content Engine Web Services (CEWS) which allows custom application to access CE using Web Services.

Clients of the Content Engine .NET API, and COM Compatibility API must use the Content Engine Web service.

As CE is build in J2EE and EJB transport allows very easy and fast connectivity to CE, Java is commonly used for custom application.

FileNet Workplace, BPF, Records manager etc are all J2EE applications and to enhance them or customize then, Java technology is preferred.

As such, FileNet doesn't restrict the developers to use Java or .Net. You are free to use the technology which is convenient to you but as FileNet's most of the components are build in Java, it makes interoperability easy for application designed in Java or J2EE.