It depends a lot on your NFL Stadium(Having been to games in Green Bay and Kansas City I would argue that those crowds are as good or better than the college games I've been to), but in general:

-Fans feel more connected to the team, as students a lot of us know our college athletes, and even if we don't we feel more connected to them than pro athletes because they're students like us. Schools also do a good job of making fans feel like they, in some ways, own or are a part of their team, and they feel more responsible for supporting them because of this.

-Greater sense of community overall, and with it community pride. As a college student I can say that our school has driven home the idea that this team, in many ways, belongs to and represents us, they're a public face of our school and their accomplishments make the university as a whole look better.

-More well established traditions. NFL Teams usually have one or two trademark traditions, but colleges make a big point to reinforce and pass along traditions, so where at an NFL game you might see one or two interesting traditions, at a college game you're likely to see half a dozen unique chants, taunts, and celebrations that have been passed on for years. To put this in perspective, when I lived in St.Louis I went to a lot of Rams games and while you could argue they haven't been around long enough to establish traditions, the only one I can think of is 'The Bob and Weave', by contrast, here in Kansas(where there are hundreds of years worth of traditions) we have the Rock Chalk Chant, the clapping during the fight song, Waving the Wheat, and tons of other traditions that I'm not sure have names. These traditions not only add to the atmosphere of the game, they enhance the sense of community and make the game feel even more intimate and intense than it would normally be.