"but, thinking that perhaps his fondness for the Dodger and the other boys, cost him a good deal of money..."
See in text (Chapter IX)
Fagin really is fond of boys, but being a wicked character he likes boys who are wicked and encourages them to be so by rewarding them with his affection. He is using that technique on Oliver from the beginning of their relationship, always calling him "My dear." This kind of treatment has a conditioning effect on the boys, making them equally fond of Fagin, who is a substitute for the fathers most of them have never known.