According to this article and this article, Coach Linehan, who grew up a Niners fan, said that "personal considerations prevent him from moving west."
"The timing is just not right. There are just some personal things I need to get ironed out. It seems like at 25, your decisions are practically made for you as you move up. At 45, it's not so easy. It's a little more complicated when you have a wife and three kids.
The job itself was outstanding. It was very, very hard (to decline). Timing-wise, it's not good. At this point, I'm not ready to make the call. It's all personal from my standpoint. My eighth-grader has been in seven different schools since he started elementary school. Some people might say that's child abuse. I'm always the one who seems to be screwing it up. We chose coaching."