I believe, 3 important aspects govern objects and their usage:
1. Instantiation (of a class together with initialisation if any).
2. Injection (of the instance so created) where it's required.
3. Life cycle management (of the instance so created).
Using Factory pattern, the first aspect (instantiation) is achieved but the remaining two is questionable. The class that uses other instances must hardcode the factories (instead of instances being created) which hinders loose coupling abilities. Moreover, life cycle management of instances becomes a challenge in a large application where a factory is used in multiple places (particularly, if the factory doesn't manage the life cycle of the instance it returns, it gets ugly).
Using a DI (of IoC pattern) on the other hand, all the 3 are abstracted outside the code (to the DI container) and the managed bean needs nothing about this complexity. Loose Coupling, a very important architectural goal can be achieved quiet comfortably. Another important architectural goal, the separation of concerns can be achieved much better than factories.
Whereas the Factories may be suitable for small applications, large ones would be better to chose DI over factories.