I still think at the end of the day, they trust their scouts. As Rodgers drops, I think the teams that skipped weren't scared at the people in front passing, they just didn't like him for whatever reason.
I have said it from day one Rodgers even though he was slated first round and had a good college career was still super raw. He had his flaws that did scare some teams away and there were a lot of teams at that point that didn't really need a first round QB. He landed in the ideal situation where he could sit behind someone for a few years learn, touch up those rough edges than start when it was his time.
I always figured that if the 49ers did draft Rodgers number one he probably have been in the same situation as Alex Smith was and would have been considered a bust.