Because the alternative is even worse?
Because we don't need to have happen to the Hawkeyes what happened to PSU when Clifford went down?
Because a QB controversy is WAY more than just subbing a backup in?
Doing that mid-season is sending a clear message to your players and locker room that you as a coach have reached the point that you have no idea what is wrong or how to fix it. Changing QBs halfway through the season is an absolute last resort and you don't do something fucking stupid like that unless the season is already lost. I don't know if you've played team sports, but even at the high school level those things cause rifts in your team. It's not good.
What do you do then if it doesn't work? What if Padilla stinks the joint up worse than Petras? At that point you've completely lost control of the situation. You think you're just gonna put Petras back in and everything will be hunky dory like you never benched him in the first place?
The Hawks are still in first place right now, and Purdue isn't going to beat OSU and MSU. We already can't run the ball, what would subbing Padilla in prove? he can get back to the LOS instead of lose 5 yds every time he gets pressured because of our terrible OL? Yeaaaaahhhh. That'll fix the problem. I don't know if you watch Padilla in the spring game, but he's not exactly John Elway and he's definitely not a better passer than Petras.