How, exactly, does that harm the NFL? If anything, it'd raise the value of the advertising time (since you'd have more of a captive audience in cinemas, with less ability to avoid the commercials).
It does a couple of things:
1 - It's somebody making money using the NFLs logos without the NFL getting any money.
2 - It's bad for the ratings, the whole Neilson machine is built around some pre-set number of people per set. if you've got movie theaters filling 700 and 800 seat auditoriums to watch the game all over the country it's probably going to hurt the Neilson numbers, which might hurt the networks (those number by and large dictate how much you charge for advertising), which will hurt the NFL (damage to the SB gravy train will reduce how much the networks are willing to pay the NFL). They might be able to work with Neilson to slide the scale to slide the scale for extenuating circumstances, although one of the things that keeps Neilson so powerful is they have a rep for not messing with the numbers for any reason.