Jim Harbaugh doesn't have a very tough decision to make, at least according to the many college and NFL coaches I have spoken to over the years.
With few exceptions, they have all told me that the NFL is the place they prefer to be. In fact, it's pretty much unanimous among the assistants. It's a lifestyle thing.
That's not to say Harbaugh won't take the University of Michigan job that reportedly was offered to him to the tune of $48M over six years. He very possibly could. If he did, that wouldn't just make him the highest paid college football coach -- it would put him on par with the highest paid coaches in all of North American sports. Now, given that scale, if he were inclined to go in that direction, wouldn't he have accepted the offer already? How much more could he possibly want?
For Harbaugh it could be personal, not just about dollars. His dad coached at Michigan. He played at Michigan and still has strong ties there.
There are certainly other reasons why a head coach would choose the college game over the NFL. You have more control. You are the big fish in the small pond of whatever college town you are in. Plus, the ability to recruit an extremely talented group of potential future first round picks each and every year could be appealing. There's no salary cap to have to worry about. (Matt Brown also wrote a piece on why the Wolverines would be a perfect fit for Harbaugh and vice versa.)
College can also be a refuge for those who are floundering on the NFL stage and may want to regroup. Remember that Super Bowl-winning coach Pete Carroll has gone back and forth, as has Nick Saban, who had a brief, unsuccessful stint with the Miami Dolphins in 2005-2006. It's been a tough year for Jim Harbaugh in San Francisco, but he did take the 49ers to three straight NFC Championships. It's possible, though, that with his front office relationship reportedly damaged beyond repair with the Niners and the other options in the NFL coaching carousel involving potentially long rebuilding processes (the Raiders, Jets, etc.), Harbaugh may see Michigan as the best bet.
The problem is that there is really no break or reprieve in the college game, if you want to have success. I talk with college coaches because of my business, Go Big Recruiting, all the time and they tell me that recruiting never stops at that level. Ever.