There is iReferee (a bit poorly rated) and Sports Rule Books which are both free apps, but the better and more straight-forward app solution to what you're looking for is American Football -Understanding the Game, which cost 99 cents. It's easy to understand (for Football newbs if you will) and has pictures and everything. You can also go to
http://www.nfl.com/rulebook to read the NFL rule book, and this page also has a free PDF download which you can read on your iDevice.
The penalties which are levied against players for certain offenses as well as a few other subtle rules vary slightly across the NFL, college football, and generic high school football, but the basic rules of the game are still the same no matter what. Once you've watched a number of games you'll easily understand the most basic rules and strategy of the game, while the different penalties (holding, pass interference, face mask, illegal formation, etc) can take a while to soak in.