There are some samples that might help here: jboss-jdg-quickstarts/Memo.java at jdg-7.1.x · jboss-developer/jboss-jdg-quickstarts · GitHub
The indexing is controlled with annotations, which are very similar (but not really 100% identical) to the annotations used by Hibernate Search for the exact same purpose.
To add indexing for a type you'll have to add @Indexed annotation to the message type declaration, then for each field that you want to index you'll have to add @Field annotation. If annotations are missing, no indexing happens. The annotations are added in the last line of text of each a documentation comment for the type/field in question.
I tried to locate the documentation for the Protobuf annotations in our user guide but could not find it. Another place were this is documented is in the javadoc of this class: infinispan/IndexingMetadata.java at master · infinispan/infinispan · GitHub
And another note on this subject, Infinispan still supports an old and deprecated way of setting up indexing of protobuf types: adding NO annotations at all. If you do not add any annotations the type in question is fully indexed (all its fields), but this is not a recommend way of doing things and will be removed in next major version.