To tie together what others have already stated or hinted at, the rules by which JAXB XJC decides whether or not to put the @XmlRootElement annotation on a generated class are non trivial (see this article).
@XmlRootElement exists because the JAXB runtime requires certain information in order to marshal/unmarshal a given object, specifically the XML element name and namespace. You can’t just pass any old object to the Marshaller. @XmlRootElement provides this information.
The annotation is just a convenience, however – JAXB does not require it. The alternative to is to use JAXBElement wrapper objects, which provide the same information as @XmlRootElement, but in the form of an object, rather than an annotation.
However, JAXBElement objects are awkward to construct, since you need to know the XML element name and namespace, which business logic usually doesn’t.
Thankfully, when XJC generates a class model, it also generates a class called ObjectFactory. This is partly there for backwards compatibility with JAXB v1, but it’s also there as a place for XJC to put generated factory methods which create JAXBElement wrappers around your own objects. It handles the XML name and namespace for you, so you don’t need to worry about it. You just need to look through the ObjectFactory methods (and for large schema, there can be hundreds of them) to find the one you need.