I always wondered about this too. From Burger King's mailbag:
IT'S BEEN THIS WAY SINCE THE MERGER.
From Scott Gibson, of Billerica, Mass.: "I've never understood the rationale behind having the "away network" televise inter-conference games (like having CBS show the Pats at 49ers). Why wouldn't they have the home team's network televise the game? That way CBS would only have to worry about working in 16 stadiums, and Fox would only have to worry about 16. But why have a system where they both have to cover all 31 stadiums? Seems like extra work shuffling equipment around the country. Do you know why this is?''
Good question, Scott, and one I had to ask the league myself. Back in 1970, this policy was adopted because all games were not sellouts in those days. Since every team had to have all its road games televised back to the home market, it made sense for the road TV network to do the game in the opposite network's stadiums. In your example, for instance, CBS does the Patriots at San Francisco because in the event that the game is not a sellout, CBS would have to have the game on in the Boston-Manchester-Portland-Providence-Hartford markets because New England, being an AFC team, is a CBS team.