Minnesota has won more National Championships than Nebraska...but that past doesn't mean much for them right now. The OP is correct. Iowa is a better program right now and has been for 8 years, which is a pretty long time.
Nebraska does have it's hype machine working which is big in college football. But they are over rated. Everyone talks about how great a job Pelini has done, but the fact remains that he doesn't have a single significant win (or at least a win over a team that has finished the season ranked).
They played a cupcake schedule last year and still lost 4 games, including to Iowa State. And they lost a lot on D, including their best player...yet somehow they are ranked in the top 10 in the country.
They have another cupcake schedule this year. I see this being 9 years in a row where they don't beat a team that finishes the season ranked.