Pa initially was upset merely because Dave hadn't gotten home from school in time to do his chores. "What in th' world has kept you so? Why ain't you been here to help me with this work?"
After Dave tells Pa that he is late getting home because he was working off his debt to Professor Herbert, a consequence of the broken cherry tree during the school field trip, Pa's anger shifts. He is upset with Professor Herbert, first because he wasn't keeping the students in school and learning in the only location where Pa thought education could take place. Then he became offended because the Professor singled Dave out to work off the cost of the damages.
Poor man's son, huh," says Pa. "I'll attend to that myself in th' mornin'. I'll take keer o' 'im. He ain't from this county nohow. I'll go down there in th' mornin' and see 'im. Lettin' you leave your books and galavant all over th' hills. What kind of a school is it nohow! Didn't do that, my son, when I's a little shaver in school. All fared alike too.
This was the real issue - that Dave was being treated differently from the other boys due to his inability to simply pay the Professor the dollar. "He ain't got no right to keep you in and let the other boys off jist because they've got th' money!"