Who didn't see that result happening? The voting was relatively close, with the Brotherhood showing 52% of the vote over the former Mubarak prime minister. Whether this will spur on new protests is now the question at hand. The other question is how the US and other countries will respond now that the military has effectively taken control of Egypt, again.
Leading up to the election, the Brotherhood candidate Morsi had made efforts to reach out to other groups including the Copts (~10% of the Egyptian population) and stressed that he was not seeking revenge, but rather an interest in governing all of Egypt. The Mubarak/military leadership has had limited interest in helping anyone outside of their own.
So one day after the election, we're back in a "wait and see" mode. The election settled the decision of who will be president though it also changed little, if anything. More on the new military powers via The Guardian:
Egypt's generals awarded themselves sweeping political powers in an 11th-hour constitutional declaration that tied the hands of the country's incoming president and cemented military authority over the post-Mubarak era.
The announcement on Sunday night came as early presidential election results put the Muslim Brotherhood's Mohamed Morsi ahead of his rival Ahmed Shafik, Mubarak's final prime minister and an unabashed champion of the old regime. But with thousands of polling stations yet to declare following the two-day runoff vote, the overall winner was too close to call.
Pro-change activists and human rights campaigners said the junta's constitutional declaration – which came just days after judges extended the army's ability to arrest civilians and following the dissolution of the Brotherhood-dominated parliament by the country's top court – rendered the scheduled handover of power to a democratically elected executive meaningless.