One reason why Atticus is such a special father is that he has a great deal of integrity and makes an excellent role model for Scout and Jem. Even though defending Tom Robinson, an African American man, is a very unpopular choice in Maycomb, Atticus does so anyway because he knows it's the right thing to do. He says, "Scout, I couldn’t go to church and worship God if I didn’t try to help that man" (page 108). He has a great deal of integrity and cares more about living up to his ideals than pleasing other people, so he sets a good example for his children.
Another reason he's a special father is that he encourages his children without pushing them. For example, Scout learns to read by climbing into his lap every night and reading what he's reading. He doesn't push her to read, but he gives her the right type of encouraging situation in which to learn to read naturally.
Finally, Atticus is a special father because he demands that Jem and Scout respect everyone, even people of lower social status or with whom he disagrees. For example, he forces Jem to apologize to Mrs. Dubose, who is a nasty and cranky older woman who berates Jem and Scout in part because Atticus is defending Tom Robinson. Even though what Mrs. Dubose says is offensive, Atticus forces Jem to apologize to her (and later Jem has to read to her), as Atticus demands that his children treat everyone with respect.