Moral excellence is rare because self-interest is an imposing force that shapes behavior in ways that are not always aligned with moral excellence. True moral excellence requires or implies a degree of selflessness and an interest in the greater good. This trait often runs directly counter to self-interest.
There are many situations where moral behavior is in keeping with self-interest, of course. In these situations it is easy to do the moral thing. A person does not need to possess moral excellence to share part of a sandwich when his fridge is full at home. It's when there is no food in the fridge at home when sharing that sandwich becomes difficult...
The thing that makes friendships of moral excellence rare is that it is said to be rare to meet a individual possessing moral excellence. Moral principles are those that identify and distinguish right and wrong. "Moral excellence" suggests that there are levels at which this recognition and distinction of right and wrong may function. Therefore, while most people you meet may be moral people who recognize and distinguish right and wrong, individuals who do so with excellence (i.e., surpassing superiority) are as rare in life as an individual who performs any other task or function with excellence. As a result of this scarcity in moral excellence (surpassing superiority), friendships of moral excellence are equally rare.
This could easily be a discussion topic, because I suspect no two people would answer the question in the same way. Probably the main reason for the differences would be that no two people would have the same opinion as to what constitutes "moral excellence."
One of the factors that distinguishes humans from other animals is our ability to think and decide for ourselves. This creates unique perspectives within every individual - personal viewpoints regarding basic philosophical questions such as what are positive moral qualities, how should one act to exhibit constructive character traits, and so on. If each of us bring our own interpretation to the answering of these kinds of questions, it becomes rare to encounter another individual whose personal opinions are close enough to our own to allow a deep friendship based on mutually shared traits to develop. That's what makes friends of moral excellence so rare - and so very special when you are fortunate enough to find one.