NH and SC were penalized too. Every state holding a primary before Feb. 5th was penalized by the GOP. They have no special exemptions for IA or NH or any other state.
The thing is that no one ever expected that either nomination contest might turn out to be so close that the *delegates* of any one state might tip the balance between one candidate and another. What the states holding January primaries were hoping for was that they would be influential because of the momentum that they'd provide, not that they'd provide a decisive number of delegates.
The key is momentum, which is not always a win. In Iowa, Huckabee had momentum from the win, and Romney lost momentum by losing to Huck by 9%. The twist was that McCain got a boost by placing 4th, nearly reaching Thompson's 3rd place total. McCain's move up helped provide additional momentum into NH. IA and NH have regularly provided momentum not just for the win but for beating expectations.