Let's have a look at what Mr Bennet actually says to Mary in the passage alluded to in the question:
[Elizabeth] looked at her father to entreat his interference, lest Mary
should be singing all night. He took the hint, and when Mary had
finished her second song, said aloud,
``That will do extremely well, child. You have delighted us long
enough. Let the other young ladies have time to exhibit.''
While this leaves some room for interpretation of exactly how harsh he is, we do already know that he has quite a satirical tongue. Furthermore, the part "extremely well" marks that he thought that she has gone to some excess, and to "exhibit" is certainly not a good thing! Consider, for example, this passage a bit later:
To Elizabeth it appeared, that had her family made an agreement
to expose themselves as much as they could during the evening,
it would have been impossible for them to play their parts with
more spirit, or finer success; and happy did she think it for
Bingley and her sister that some of the exhibition had escaped
his notice, and that his feelings were not of a sort to be much
distressed by the folly which he must have witnessed
Mr Bennet's speech is not very civil, and not only insulting to Mary, but also to the "other young ladies". Not a thing that a well bred man should say. Any further doubt should be dispelled by Elizabeths reaction to what he said:
Mary, though pretending not to hear, was somewhat disconcerted; and
Elizabeth sorry for her, and sorry for her father's speech, was afraid
her anxiety had done no good.
Furthermore, there is also the following part, a paragraph later, when Mr. Collins has had his turn at making a fool of himself:
Many smiled; but no one looked more amused than Mr. Bennet himself [...]
Looking amused when someone is embarrassing himself is not a sign of good breeding, especially if the person in question is a relation. This point is also reinforced by what Elizabeth herself thinks after reading the letter referred to in the question:
Her father, contented with laughing at them, would never exert himself to restrain the wild giddiness of his youngest daughters
Laughing at others is bad enough, but not to attempt to regulate the behaviour of your offspring is a serious dereliction of duty. Mr Bennet might be the most likeable father figure in Austen's finished works (hardly a tough competition), but he is like all others (Mr Morland in Northanger Abbey, whom we do not see much of, possibly excepted) still seriously lacking, having failed to prepare his daughters properly for adult life.