Didn't have a NFL size (and maybe talent) Oline protecting him against smaller weaker defenses. Played 1/4 of the season injured and didn't have to throw it against teams like BYU.
Maybe you're right, had he played a whole season against teams like yours he would have had 1,484 yards, 0 TDs, 0 INTs, but a 81% completion with 181 rating. Heck, he had to show up more for NIU and IDST.