I think NFL General Managers play moneyball all the time, they just have a different set of ground rules, including a salary cap. They are always deciding how much to commit to a backup player vs. addressing a weakness at a starting position, how long to structure contracts, whether to go young or go after veterans or mix the two. They often have to make a judgment about how much to overpay to keep a particular person off the market if the team is weak at backup for that position.
In many respects I think baseball and football have similar scouting issues in that scouts like to evaluate what they can quantify, like speed, strength, etc. but it is harder to evaluate football skill, the ability to learn, determination of a player after he gets a big money contract, etc.
Moneyball in baseball is about drafting college players when the market overvalues high school players based on "projectability", then going back to drafting high school players when the market overreacts the other way. It's about paying for the skill of getting on base when the market is neglecting that and overpaying for power instead. When he lost Jason Giambi, he knew he couldn't afford a player with a .400 OBP and .550 SLG, so he got a first baseman (Scott Hatteburg) who could replace the OBP and looked to get the power at other positions (for example Jermaine Dye). The net cost was a lot less than trying to buy a free agent slugging first baseman.
Similary, Bill Walsh used to draft players who were thought of as not big enough or strong enough or fast enough at a position, but he saw other advantages. For example he would draft a running back who was thought to be not big enough, but who could catch, and use the back on passing downs. Or he'd draft a run stuffing defensive lineman and a pass rushing lineman, and platoon them as the play dictated. He greatly increased specialization on players. Obviously he didn't invent this, but he seemed to advance it more than others.
There is a problem with committing big money at the top of the NFL draft to a rookie -- $30 million guaranteed to a top pick has to be compared with what it would buy on the free agent market instead. I think some day soon we will see "signability" picks where the team makes a deal with a player at a number before the draft and overdafts rather than committing bigger money.
