I and my brothers certainly managed to make my parents very angry with us a fair few times while growing up, but I have reason to believe they always loved us and still do. Indeed, my belief is that a child can make their parents so angry because of the love the parent bears for the child - my parents never got so angry on hearing of other, strange (to them) children doing the same things as when we did them.

And if Mr Bennet wasn't angry because of concern for Lydia, what was he angry about? He doesn't seem to be concerned about protecting the family reputation, for example he's prepared not to spend any money on Lydia's wedding clothes. He never seems that bothered by what the neighbours think. Once Mr Bennet's received Mr Gardiner's letter, he has reason to be angry at Lydia at imposing all these costs on her uncle, but Mr Bennet charges off to London well before that happens.