I don't believe the league outright fixes games to have a predetermined winner or preferential winner. I also don't generally believe they care who wins the games, though on a rare occasion they may. I do believe the league works over the Lions not on an intentional basis, out of malice. Rather they do it because we historically haven't stood up for ourselves on the field or behind the scenes it would seem. Think back to the picked up flag in Dallas or the batted ball in Seattle. If those incidents happened to a Dan Campbell coached team he'd be red in the face, screaming in the refs ear, and blowing them up for the remainder of the game. Jim Caldwell just stood their stone silent and took it, no questions asked. I also feel that Sheila and Rod, unlike her father, mother, or Tom Lewand, would be raising hell behind the scenes and privately demanding answers from the league. So because we never used to stand up for ourselves as an organization, the league and its officials just didn't take us seriously.
If the league did prefer the 49'ers over us I would have to guess it would boil down to money. The 49'ers are in a much bigger metro market and rank in the top 5 in merchandise sales. They are also top 10 in revenue for the league and we are the dead last franchise in revenue. They are a top 5 franchise in overall value and we are at the bottom. Our fans also spend middle of the pack on merchandise and some of the least on concessions at a game. We're blue collar and some white collar fans, with not nearly the amount discretionary spending that the average 49'ers fan would have to spend on merchandise, tickets, concessions, etc.