Tens of thousands of Syrians gather for a pro-government rally at the central bank square in Damascus March 29, 2011. Syrian President Bashar al-Assad accepted his government's resignation. (REUTERS)

When anti-government protesters buried their dead last week in southern Syria, their chants made clear that the divisions now coursing through Syria run even deeper than politics.

“No Iran,’’ they shouted. “No Hezbollah. We want Muslims who fear God.’’

To anyone listening, the message was unmistakable: that the quest to topple the Assad family also reflects years of pent-up grievances among majority Sunni Muslims who resent the power held by the minority Alawite sect.

That sectarian tension lies behind some of the passions now exploding in Syria as President Bashar al-Assad seeks to appease an angry population. But it also explains the apprehension being voiced by many Syrians uneasy about where a struggle for power might lead.

On Tuesday, as Assad offered new concessions to his opponents, thousands of Syrians gathered in downtown Damascus to show support for a leader whose family has kept a tight lid for more than 40 years on a country with a potentially explosive mix of religious sects and ethnicities.

Assad hails from a dynasty of Alawites, the minority sect that makes up no more than 16 percent of Syria's population of mostly Sunni Muslims with a sprinkling of Christians and Druze. The challenge now being mounted by opponents is the most serious yet to the Assads’ grip on power, but it is also prompting warnings that any regime change in Syria could ignite internal violence.

“The Syrians have looked into the abyss, and they realize that Bashar al-Assad is not going to step down, that the Alawite regime is not going to go away, and in order for it to go away, they would have to go through a civil war,’’ said Joshua Landis, a Syria expert at the University of Oklahoma.

Activists say the government is trying to ignite unease by portraying their democratic movement as a sectarian one. The government has described the protests as a foreign “conspiracy” and a “project to sow sectarian strife.”

But there is evidence that the possibility of such clashes has unnerved some Syrians.

The Sunni Arab elite of Syria largely supports Assad, seeing him as an agent of stability and economic reforms. That is now threatened as foreign companies begin to pull out their staffs and tourists flee.

Religious minorities worry that if the Sunni majority came to power, Syria could become a repressive Islamic state. They would rather continue to live under the current system, sacrificing their freedoms in a secular and repressive state, than risk what might follow if Assad is ousted.

“As a minority we know that under a regime that is also a minority at least there is a secular system we’re comfortable to live under,” said a Christian resident of Damascus.

“Now it is pretty safe and people do not have problems with each other,” he said. “That’s because we know in the back of our minds if sectarian violence did break out it would be bad and it would be long term.”

Protesters have continued to press for reforms. On Tuesday, Assad accepted the resignations of his cabinet ministers, as he sought to contain the most serious threat to his rule since he assumed power nearly 11 years ago.

The action, reported on state TV, marks the latest concession by Assad since protesters forced a string of political promises from his government, including a pledge to lift a 48-year-old emergency law. On Saturday, Assad released hundreds of political prisoners and pulled back security forces from the city where Syria’s unrest began this month.

On Tuesday, Secretary of State Hillary Rodham Clinton expressed “strong condemnation of the Syrian government’s brutal repression of demonstrators” who had joined the uprising. But the Obama administration has made clear it has no plans to press for a no-fly zone similar to the one in Libya.

“Our preference is to let these things play out as a Syrian process, not one imposed by us,” said one administration official, speaking on the condition of anonymity to candidly discuss policy.

So far, the Syrian opposition has tried to keep protests united under the banners of freedom and nationalism. But as anger grows over violent government crackdowns that have killed at least 60 people, an undercurrent of sectarianism is slowly bubbling up.

The chants of mourners last week in Daraa, the center of the burgeoning unrest, revealed the majority’s anger at being ruled by a minority religious group, and at their leaders’ close ties to Shiite Iran and to Hezbollah, the Shiite militia in southern Lebanon.

And last weekend, armed men rampaged through the port city of Latakia, where Alawite communities surround a predominantly Sunni city center that has a small community of Christians. At least 12 were killed in the rare outbreak of violence.

“There is the fear of sectarianism, and then there is the fear of the regime,” said Yassin Al-Haj Saleh, a Syrian intellectual and member of the opposition who was imprisoned for 16 years.

“This type of thing pushes many people to identify with the regime, to ask for protection from the regime, and the regime is completely aware of this,” he said. “This is their strategy.”

Ghimar Deeb, a lawyer in the capital, dismissed the idea of underlying sectarian tensions and said Assad needs time to implement reforms. “I believe this case that we’re living through right now will make Assad and Syria stronger and more Syrian,” he said.

Staff writer Mary Beth Sheridan in Washington contributed to this report.