Video games are a different beast, yes.
That said, how is the NFL hurting themselves? They are getting their money from EA, and their brand is being represented by a product which sells very well and the critical consensus of said product is that it is at least "good", sometimes "great".
If Madden were truly seen by the vast majority of people as a low-quality product, the NFL might consider changing partners. Currently there's no reason for them to do this.