I think people are asking all the wrong questions. Let's put aside the Muslim Brotherhood boogey man theory and consider the aftermath of this riot. Who is capable of governance in a country where authority stemmed from an authoritarian source? What could the post-Mubarak gov't possibly do to curb the rising unemployment and heal the battered economy?
I feel expectations will be unrealistically high for any incoming administration and may create further resentment rather than void it.
The Muslim Brotherhood can't really just been thrown off as a "boogey man" since they're the most organized opposition in Egypt. So far, the protests have had no leaders and have just been a popular protest. There's no means of organizing them into any form of political party or government without someone able of drawing support internally and, to some extent, internationally. A power vacuum would be just what the MB wants since it would give them the best chance of establishing themselves in power.
The same goes for Tunisia. Without any popular agreement or organization, they are dependent on existing political parties who have organization and resources on their side.
It'll take time for other groups to really establish themselves to challenge parties already in existence.