I would say yes, it is appropriate for a repository to have methods for retrieving aggregates by something other than the identity. However, there are some subtleties to be aware of.
The reason that many repository examples only retrieve by ID is based on the observation that repositories coupled with the structure of aggregates cannot fulfill all query requirements. For instance, if you have a query which calls for some fields from an aggregate as well as some fields for a referenced aggregate and some summary data, the corresponding aggregate classes cannot be used to represent this data. Instead, a dedicated read-model is needed. Therefore, querying responsibilities are decoupled from the repository. This have several advantages (queries can be served by a dedicated de-normalized store) and it is the principal paradigm of CQRS. In this type of architecture, domain classes are only retrieved by the repository when some behavior needs to execute. All read-only use cases are served by a read-models.
The reason that I think it appropriate for a repository to have a GetByEmail method is based on YAGNI and battling complexity. You an allow your application to evolve as requirements change and grow. You don't need to jump to CQRS and separate read/write stores right away. You can start with a repository that also happens to have a query method. The only thing to keep in mind is that you should try to retrieve entities by ID when you need to invoke some behavior on those entities.