To me, this is mostly due to putting too much on the QB's plate. Golson was good in 2012 when they relied on the running game, but struggled in 2014 when the whole offense was put on his shoulders. Same thing with Kizer in 2015 and 2016. I think the problem with Wimbush was simply that defenses figured out he couldn't reliably hit short passes so they stopped defending them.
With Book, it is similar to 2014 and 2016. They are putting too much on him. Last year defenses had to account for Dexter Williams. This year they aren't respecting the run. Some of that is RB talent, but ND has enough OL talent to overcome that and Tony Jones is a fine college RB.
The solution is to rely on the run game more with Jones and Smith (who should be healthier) . A more conservative, ball control offense also complements the defense better.