So the rebels aren't secular Jeffersonians. As far as America is concerned, it doesn't much matter.
By all accounts, Sunni Islamists are leading the fight against Syrian President Bashar al-Assad and are on track to become the paramount political force in Damascus after he's gone. The mainstream Syrian Muslim Brotherhood dominates the Syrian National Council, the opposition's primary political umbrella and diaspora fundraising arm, while more militant Salafi-jihadist groups are assuming a steadily greater role in fighting regime forces on the ground. Even the supposedly secular Free Syrian Army (FSA) is exhibiting an Islamist character, with one leading commander recently exhorting Syrians to "go for jihad" and "gain an afterlife and heaven." Many outside observers find the Islamist character of the revolt disconcerting, with some even counseling indirect U.S. military intervention as a means of suppressing it.
Unfortunately, there's not much the United States can do about it. Islamist political ascendancy is inevitable in a majority Sunni Muslim country brutalized for more than four decades by a secular minoritarian dictatorship. Moreover, enormous financial resources are pouring in from the Arab-Islamic world to promote explicitly Islamist resistance to Assad's Alawite-dominated, Iranian-backed regime. Providing "secular" rebels with additional money and arms won't reverse the effects.
Fortunately, while the Islamist surge will not be a picnic for the Syrian people, it has two important silver linings for U.S. interests.
For starters, the Assad regime would not be in the trouble it's in today were it not for the Islamists. Though the March 2011 uprising was initially broad-based, the Arab world's most sophisticated internal security apparatus easily pacified protesters outside of heavily Sunni areas. But the mixture of faith and politics proved impossible to contain: Since banning Muslims from attending prayers was politically unthinkable, mosques became the focal points of massive anti-government demonstrations that quickly overwhelmed the regime's capacity to clear the streets without bloodshed.
Islamists -- many of them hardened by years of fighting U.S. forces in Iraq -- are simply more effective fighters than their secular counterparts. Assad has had extraordinary difficulty countering tactics perfected by his former jihadist allies, particularly suicide bombings and roadside bombs. The Islamists' ability to shatter the calm even in high-security neighborhoods of Damascus and Aleppo is slowly stripping away the regime's outer layers of non-Alawite support. Militant Trotskyists just don't pack the same punch.
The Sunni Islamist surge may also be essential to inflicting a full-blown strategic defeat on Iran. Once the regime is toppled, Assad and his minions will likely retreat to northwestern Syria, where non-Sunnis are (barely) a majority. This could result in a rump state in the Alawite heartland, secured by chemical weapons and Iranian-supplied resources and arms. For all of their faults, Sunni Islamists hell-bent (or heaven-bent) on purging the country of Iranian influence can be counted on to reject a "no victor, no vanquished" settlement like the 1989 Taif Accord, which brought Lebanon's civil war to a halt but institutionalized its political fragmentation and loss of sovereignty.
While there is sure to be regional spillover, it will cut mainly against Tehran. There will be tough times ahead for Lebanon, but ultimately the Assad regime's death throes can only work against the Shiite Hezbollah movement. Iraq's ruling Shiite leadership, hitherto sycophantic where Iranian interests are concerned, may find it necessary to distance itself from Supreme Leader Ayatollah Ali Khamenei's more unpopular Arab clients. With its own restive Sunni minority, Iran itself could be severely rattled by sectarian blowback.
Of course, Syrian Islamists are no friends of the United States -- merely the enemies of one of its enemies. Indeed, their long-term aspirations are arguably more reprehensible than those of the mullahs in Tehran -- Shiites, after all, aren't obsessed with converting others their faith. Syrians have also been prominent in the leadership of al Qaeda, easily recognizable by the surname al-Suri in their noms de guerre: Notable examples include Abu Musab al-Suri, a major al Qaeda ideologue; Ghazawan al-Suri, the leader of al Qaeda in Mosul captured in 2007; Abu Zaid al-Suri, a deputy leader of al Qaeda in the Iraqi town of Rawah, captured in 2006; Abu Layla al-Suri, the leader of al Qaeda in Diyala, killed in 2008.
For the foreseeable future, however, Iran constitutes a far greater and more immediate threat to U.S. national interests. Whatever misfortunes Sunni Islamists may visit upon the Syrian people, any government they form will be strategically preferable to the Assad regime, for three reasons: A new government in Damascus will find continuing the alliance with Tehran unthinkable, it won't have to distract Syrians from its minority status with foreign policy adventurism like the ancien régime, and it will be flush with petrodollars from Arab Gulf states (relatively) friendly to Washington.
So long as Syrian jihadis are committed to fighting Iran and its Arab proxies, we should quietly root for them -- while keeping our distance from a conflict that is going to get very ugly before the smoke clears. There will be plenty of time to tame the beast after Iran's regional hegemonic ambitions have gone down in flames.