org.springframework.data.annotation.Id is currently used by Spring to support mapping for other non relational persistence databases or frameworks that do not have a defined common persistence API like JPA. So, it is normally used when dealing with other spring-data projects such as spring-data-mongodb, spring-data-solr, etc.
javax.persistence.Id is the annotation defined by JPA for all its implementations. Have in mind JPA only applies for management of relational data.