Lots of rationale for it in my opinion. I root local more than I root for some team I've never seen and have no hope to see in person. Conference contains my team's wins. The better they look, the better my team looks. Conference is more likely to contain local players.
Might be a product of being a fan of a smaller conference team that I grew up with.
It's kind of funny thinking about it. I'll root for my alma-mater (B10) over most teams. But the team I grew up with (Toledo), I'll root for them over my alma-mater in most cases. I'd root for Toledo over the big three, Ohio St, UM, ND, unless something important was on the line not available to Toledo, like a chance an NC. I was rooting for Northern Illinois. a conference member, over ND.