I live in an NFL time as well, and it hasn't affected my feelings at all towards BYU football.
If cheering more for an NFL team lessened your emotions towards BYU football, then I'd say your feelings towards BYU football probably weren't as strong as you may have thought.
Just by two cents. Glad you've gotten into an NFL team. I'll say, it is fun and exciting to be in a town that truly loves the local professional teams, and it's fun to go to the games.