I think there a few things at play:
#1: The ratings for live TV overall are down from previous years. That applies to sports and non-sports. That's a function of the fact that more people are busy doing other things and can't devote 3 hours to being couch potatoes. So they'll DVR and watch later, or maybe DVR and not actually watch because they already know the final score.
#2: The match-ups for the NFL national games, primarily for the first half of the season, haven't been good. I look at the upcoming games, and if they don't include teams I'm interested in, I don't watch. Lots of other choices for my team. The second half of the season, NBC has the right to adjust the Sunday night match-ups, so the teams are more involved in play-off situations, and they're just better teams at that point.
#3: Yes the NCAA games are better, especially now. Consider Tennessee vs. Georgia. That game was one example, but there were a whole bunch where the lead changes so many times, so many unpredictable moments, so much fun and excitement. Even if you don't have a dog in the fight, which is my situation, the games are fun. But that doesn't necessarily mean they translate to better ratings, because of my first point, and they're not taking viewers away from the NFL. As the season goes along, the prime time matchups will improve, the weather will get colder, and I expect NFL ratings will improve a little, although they'll probably still be lower than last year.