"There is little friendship in the world, and least of all between equals, which was wont to be magnified. That that is, is between superior and inferior, whose fortunes may comprehend the one the other."
He is saying the best basis for friendship is a mutual interest shared between a higher status person and a lower status person.
There is little friendship in the world,
There is little friendship in the world
and least of all between equals,
and there is least friendship between equals,
which was wont to be magnified.
which (friendship between equals) has been usually highly praised.
That that is,
The friendship that does exist,
is between superior and inferior,
is between principal and subordinate
whose fortunes may comprehend the one the other.
whose best interests may be mutual.
It's a criticism on social classes. What seems to be friendship is nothing but a relationship between superior and inferior, or poor and rich, and you can even extend that to race in our contemporary time.
The entire structure of a poor person's discourse and language, including his beliefs and values, is done so, according to Bacon, with the comprehension of fortune in his mind, specifically that he has none or very little, with respect to the rich person. The same is done for the rich person who in turn has a relationship with a poor person.
It seems to me that it means: Friendship between equals is nothing special. It does not deserve to be extolled. The friendship which is to be extolled ("that that is [wont to be magnified]" = that friendship which is deserving of praise) is the friendship between people of different status, where each fully understands the fortune of the other so different from himself.