Why did he say "who is their father"?
Rashi (from Tosefta Bava Metzi'a 3:14): He rebutted their astonishment ("l'Ven Kish... ba'Nevi'im"). Is prophecy an inheritance?!
Radak citing Targum Yonasan: Who is their Rebbi? Who taught these Nevi'im, and put Ru'ach of prophecy on them? Hashem! If so, it is not astounding if also Sha'ul [has prophecy].
Chomas Anach: Did they merit due to their fathers? Perhaps it is in their own merit. Perhaps Sha'uls merit (he grabbed the Luchos refer to 4:12:1:1] joined to his grandfather's merit!
Malbim: He refuted their assumption that natural preparation must be from the father. Who were the fathers of Bnei ha'Nevi'im? They were not Nevi'im, for prophecy was rare in those days! The only Chidush is that Sha'ul reached prophecy without preparation via choice. Therefore, they omitted mention of Ben Kish in the metaphor.
When would people say "ha'Gam Sha'ul ba'Nevi'im"?
Radak: From then and on, when a lowly person rose.
Malbim: It was when someone reached prophecy without preparation via choice.
