At the same time, I can understand it was easy to underestimate the weight of the Brotherhood, with medias playing on the name of El Baradei and other secular figures. I agree with your point that it could have been a lot worse.
In Egypt at least, the Muslim Brotherhood had a number of pretty significant advantages compared to liberals and secularists. Whereas Mubarak basically crushed secularist dissent, he seemed to tolerate the Muslim Brotherhood (on a very short leash) for use as boogeymen. They were also able to organize in mosques, which were more or less untouchable, whereas nobody else had such a safe place to organize. Finally, the Mubarak regime was largely secularist, which tainted other liberals by association.
The end result was that, after the revolution, the Muslim Brotherhood had a very well-organized political network ready to go, while everyone else was going, "Hmm ... time to form a political party. How do we do that?"
Maybe I'm just an old cynic, but expecting the best possible outcome from a revolution seems naive. It's what everyone goes in hoping for, maybe what the revolting masses intend, but in the power vacuum that follows then someone or some group will fill it with a 'strong' leader. This leader then proceeds to take the place in his own direction, usually protected by a combination of true believers and self-interested hangers-on. Which then screws over most of the people that got them there. Look at the Iranian revolution - many female students took part in that one, only to find themselves far worse off afterwards.
The fact we only have a potential despot in Egypt so far is actually really positive!