First, the Muslim Brotherhood often mobilizes supporters over animosity towards the West. This animosity is based on historical injustices as well as a perceived Western antagonism towards Islam. However, by legitimizing the ability of the Brotherhood to follow democratic principles, the United States has taken some of the wind out of the sails of this argument. In fact, U.S. support of the Brotherhood's presence in elections is a more tolerant position than that of some very secular Egyptians.
Second, and perhaps more cleverly, the United States has sent the Brotherhood a message about its expectations. Saying that the Brotherhood can maintain democratic principles is a subtle message that the United States expects the Brotherhood to do so. It also communicates that so long as the Brotherhood maintains these principles, it will not face direct resistance from the United States government. The statement thus sets up a clear objective, and incentives for the Brotherhood to meet this objective.
Finally, the Obama administration has begun the slow process of engaging more deeply with Egyptian society. Whether or not the administrations message was communicated directly to the Brotherhood, it is nonetheless a communication between the Brotherhood and the U.S. government. Additionally, the administration's position is relatively hands-off. It seeks to guide the outcome of elections to maintain democratic principles, but is not openly stating a preference for which party it wishes to see doing this. Its pro-democracy position is uncontroversial and the position of a majority of the Egyptian public, many of whom spent hours today waiting in line to vote in parliamentary elections.
Ultimately such pragmatic statements will serve the United States well in its engagement with the post-Mubarak Egypt and the post-revolution Arab world. While pragmatism may involve admitting some sub-optimal realities, these admissions are the first step to crafting smart policy which will advance the interests of the United States and its allies in the region.