The fears of militant Islamists taking over Egypt turned out to be overblown. The Muslim Brotherhood has joined the democratic process and, for the most part, have not precipitated violence, so they're not the real problem. The Egyptian military is and, to date, has failed to relinquish power. Rather, they are tightening their hold on power as noted here (by the way, the Sandmonkey's offending post that caused his suspension is now here).
In Syria, militant Islamists are a more serious problem. Strangely enough, Obama and al Qaeda policy are the same when it comes to the country's dictator, although the means obviously differ. Do uppity Sunnis and al Qaeda terrorists justify the repression and oppression of Bashar al-Assad, and does this justify his remaining power? To me, no. I'll always take the risk of upending the leader of an "not free" regime for the chance of a freer society. But still, it helps to be aware that a good number of rebels don't wear white hats. It looks like this uprising will not end soon. The Iranian de facto police state is aiding the Syrian de facto police state.
Western and Arab experts and diplomats estimate that the number of troops and advisers from the Quds force in Syria to be in the high hundreds or low thousands. They have set up at least one base in Zabadani near the capital Damascus.