One of my lecturers used to use this phrase very often.
As far as I noticed depending on your voice tone it can be either a question or the illustration of your understanding.
For ex: When the lecturer is teaching the class he is giving an example about the topic and just after giving the example he is asking to class that "fair enough ?" by meaning, "did you understand why I gave this example", "did you understand the connection of this example with the topic?"
If as a student you say yes it's "fair enough", you mean that yes I understood why you gave this example.
Briefly as far as I know the phrase "fair enough" means " yes I quite understood why you did that, why you said that etc."
I am neither a native nor a teacher if I am wrong please correct me