“We staged demonstrations to get freedom, not to have an emir ruling us,” Mr. Haytham said, referring to the title used by Islamist commanders.

The collection of groups fighting the government has always been an uneasy alliance, and some rebels have long said they expected to battle the more radical groups — after defeating Mr. Assad — over their desire to monopolize power and impose religious rule. As the fighting has accelerated, the most radical groups have received the most resources from abroad, allowing them to emerge as the most successful fighting forces.

For a time, that success on the battlefield won the support of many oppositions fighters and activists, who are eager to have a powerful ally. But the prospect of victory has receded as government forces have reasserted themselves with the help of Russia, Iran and the Lebanese militant group Hezbollah. And now some rebels and activists find themselves threatened by fighters they once saw as allies.

“The sea is in front of us, and the enemy is behind us,” said Sheik Jassem al-Awad, a tribal leader in Raqqa, adding that he felt squeezed between the government and the radical Islamists. “The Free Syrian Army cannot open two fronts at once.”

Sheik Jassem spoke from Turkey, where he fled shortly after being held in a cellar for 25 days by the Islamic State. The group arrested him and eight others from an opposition media center in Raqqa and confiscated $50,000 worth of equipment, he said. One of the others, Jamil Sello, said he had several broken ribs from beatings and had been accused of “trying to establish a secular state, collaborating with the U.S. intelligence and Qatar.”

A deputy president of a Syrian tribal union, Sheik Jassem said the Islamists had looted Raqqa of cash and even machinery from its Euphrates River dams. He said that after the merger in April of the Nusra Front, the first radical group to rise within the rebel movement, with Al Qaeda in Iraq, the united group’s power had grown “like a larva transformed into a butterfly.”

“What can I say?” he added. “The worst thing is that now the regime will gloat.”

When the Syrian protest movement became an uprising two years ago, the Free Syrian Army was less an organization than a brand name for a loose collection of units formed by civilians and army defectors. The exile opposition tried to unify them, most recently under the secular-minded Gen. Selim Idris.