Story highlights Analysts say airstrikes against ISIS could play into the hands of President Bashar al-Assad

U.S. military official: "I wouldn't characterize the effects we had last night as benefiting Assad"

NYT: Benefits to al-Assad may be most "morally troubling consequence" of Obama's plan

The Western-backed rebels are fragmented and not ready to take ISIS territory, experts say

The United States has inflicted damage on one enemy in Syria with the airstrikes it launched against ISIS. But it may also be helping another foe: the regime of President Bashar al-Assad.

Now, warplanes from the U.S. and Arab nations are pummeling the stronghold of ISIS, a group that has gained global notoriety for its brutal tactics and ruthless treatment of people who don't follow its extremist version of Islam.

But ISIS, which controls broad areas of northern Syria and Iraq, has also been racking up military victories against al-Assad's troops.

The Syrian regime may end up as "the real winner" from the expanded campaign against ISIS, said CNN Political Commentator Peter Beinhart.

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The potential benefits to al-Assad from the airstrikes "may be the most dangerous and morally troubling consequence of President Obama's decision to cross the Syrian border to fight the Islamic State," The New York Times warned in an editorial Tuesday.

To try to prevent that, the Obama administration has to delicately navigate this minefield. Here are the challenges it faces:

1. Distance itself from al-Assad

The White House has been at pains to stress that the airstrikes took place without any cooperation with al-Assad's government, which has been fighting against rebel groups for more than three years in a vicious conflict that has killed around 200,000 people.

"I want to be very clear ... that we did not coordinate with them, we did not provide them advance notice of the timing or of targets that the U.S. was going to strike. In fact, we warned them to not pose a threat to our aircraft," Ben Rhodes, Obama's deputy national security adviser for strategic communications said Tuesday.

The only contact, he said, was U.S. Ambassador to the United Nations Samantha Power telling her Syrian counterpart that direct action was to be taken.

U.S. officials are also playing down the advantages of the airstrikes to the Syrian regime, although not very convincingly.

Map: Airstrikes in Syria

"I wouldn't characterize the effects we had last night as benefiting Assad," said Lt. Gen. William Mayville, director of operations for the Joint Chiefs of Staff.

2. Quickly bolster moderate rebels

The big question is that if the airstrikes weaken ISIS' grip on northern Syria, who will step in and take that territory.

In his address Tuesday, Obama emphasized intensified U.S. efforts to train and equip more moderate Syrian rebels as "the best counterweight" to both ISIS and al-Assad.

But many analysts are skeptical that the rebels will be in a position to make major inroads anytime soon. Congress only approved Obama's request to arm and train "appropriately vetted" rebel groups last week.

Photos: U.S., Arab nations attack ISIS in Syria Photos: U.S., Arab nations attack ISIS in Syria U.S., Arab nations attack ISIS in Syria – In this photo released by the U.S. Air Force, fighter jets fly over northern Iraq as part of coalition airstrikes in Syria on Tuesday, September 23. The United States and several Arab nations have started bombing ISIS targets in Syria to take out the militant group's ability to command, train and resupply its fighters. Hide Caption 1 of 13 Photos: U.S., Arab nations attack ISIS in Syria U.S., Arab nations attack ISIS in Syria – A U.S. Navy jet is refueled in flight after airstrike missions in Syria on September 23. In addition to bombing ISIS, the United States has also taken action -- on its own -- against another terrorist organization, the Khorasan Group. U.S. President Barack Obama described Khorasan members as "seasoned al Qaeda operatives in Syria." Hide Caption 2 of 13 Photos: U.S., Arab nations attack ISIS in Syria U.S., Arab nations attack ISIS in Syria – This photo, released by activists in Idlib, Syria, on September 23, shows what they say is the aftermath of U.S. airstrikes against ISIS. Hide Caption 3 of 13 Photos: U.S., Arab nations attack ISIS in Syria U.S., Arab nations attack ISIS in Syria – Another aftermath image from the Idlib activists. Hide Caption 4 of 13 Photos: U.S., Arab nations attack ISIS in Syria U.S., Arab nations attack ISIS in Syria – Obama, speaking at the White House on September 23, addresses the ISIS airstrikes. "The strength of this coalition makes it clear to the world that this is not America's fight alone," Obama said. Hide Caption 5 of 13 Photos: U.S., Arab nations attack ISIS in Syria U.S., Arab nations attack ISIS in Syria – The USS Philippine Sea, a guided-missile cruiser with the U.S. Navy, launches a Tomahawk cruise missile from the Persian Gulf during an attack on ISIS positions on September 23. The U.S. Navy released this photo and several others following the airstrikes. Hide Caption 6 of 13 Photos: U.S., Arab nations attack ISIS in Syria U.S., Arab nations attack ISIS in Syria – U.S. sailors stand on the bridge of the USS Philippine Sea while Tomahawk cruise missiles are launched toward targets in Syria on September 23. Hide Caption 7 of 13 Photos: U.S., Arab nations attack ISIS in Syria U.S., Arab nations attack ISIS in Syria – The USS Arleigh Burke, a guided-missile destroyer with the U.S. Navy, launches Tomahawk missiles in the Persian Gulf on September 23. Hide Caption 8 of 13 Photos: U.S., Arab nations attack ISIS in Syria U.S., Arab nations attack ISIS in Syria – An F/A-18C Hornet prepares to take off from the flight deck of the USS George H.W. Bush, a U.S. Navy aircraft carrier in the Persian Gulf, before conducting strike missions against ISIS targets on September 23. Hide Caption 9 of 13 Photos: U.S., Arab nations attack ISIS in Syria U.S., Arab nations attack ISIS in Syria – Tomahawk missiles fired by the USS Philippine Sea fly in the air above the Persian Gulf on September 23. Hide Caption 10 of 13 Photos: U.S., Arab nations attack ISIS in Syria U.S., Arab nations attack ISIS in Syria – Two more U.S. fighter jets prepare to take off from the USS George H.W. Bush and conduct airstrikes against ISIS targets in Syria. Hide Caption 11 of 13 Photos: U.S., Arab nations attack ISIS in Syria U.S., Arab nations attack ISIS in Syria – This before-and-after image, provided by the U.S. Department of Defense, shows what is purported to be an ISIS command center that was targeted by airstrikes in Raqqa, Syria. Hide Caption 12 of 13 Photos: U.S., Arab nations attack ISIS in Syria U.S., Arab nations attack ISIS in Syria – The Defense Department also released this before-and-after image of a purported ISIS finance center in Raqqa. Hide Caption 13 of 13

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Turning those groups into a force that can take on ISIS' feared fighters and al-Assad's military will take time. But the strikes against ISIS are happening now.

3. Manage a fragmented opposition

Experts say that the rebels fighting for the Western-backed Free Syrian Army (FSA) lack a unified leadership.

"Syria is a fragmented country, and most of these militias have a very town-centric quality. They're based on clan structures and regional structures," Joshua Landis, director of the Center for Middle East Studies at the University of Oklahoma, said in an interview with WBEZ earlier this month.

"None of them have really developed a national scope, except for the Islamist ones, like al Qaeda and ISIS," he said.

The sheer number of different militias across Syria -- estimated in the hundreds -- runs the risk of turning Syria into a patchwork of warlord fiefdoms.

"If you just give them money without unifying them, you're going to get Somalia," said Landis.

4. Juggle unaligned objectives

Keeping the rebels on board with American military objectives is also fraught with difficulty.

The initial reaction from Syrian activists to the airstrikes Tuesday was a sense of relief that the U.S. had taken action against ISIS, CNN's Arwa Damon reported. But that was before it emerged that the strikes had also hit members of the al-Nusra Front , a terrorist organization that was nonetheless among the rebel groups resisting ISIS.

That news, along with reports of civilian casualties, soured the mood among the activists, Damon reported, with apprehension growing on the ground about what intentions of the U.S. and its allies have for Syria.

The focus on defeating ISIS may also be hard to stomach for many rebels.

"We have to remember, the FSA wants to destroy Assad, not ISIS," Landis said. "They will destroy ISIS if America makes it contingent -- they don't like ISIS. But their goal, from the beginning, has been to fulfill this revolution. If their only object is to kill ISIS, many of them feel the revolution will be dead."

5. Navigate the proxy wars

The picture is all the more complicated because of the web of competing interests in the Syrian conflict.

"Syria is the biggest, most complicated proxy war in modern history," said Rami Khouri, director of the Issam Fares Institute for Public Policy and International Affairs at the American University in Beirut.

Al-Assad's regime has strong ties to Iran, Russia and Hezbollah. Various rebel groups -- some moderate, some more extremist -- have received support from the U.S., Turkey, Saudi Arabia, European nations and others.

In a conflict with so many international powers jostling for influence, contradictions like American airstrikes potentially helping al-Assad's regime become hard to avoid.

"There is no simple black-and-white, linear answer," Khouri told CNN on Wednesday.

6. Prevent chaos from spreading farther

Some analysts have also questioned whether the West wants an outright victory of the rebels over al-Assad's forces.

"America is trying to contain this problem, it's not trying to blow apart the rest of Syria," Landis said.

He noted that many big Syrian cities under the control of al-Assad, like Damascus and Hama, have been spared the worst of the violence, leaving residents relatively undisturbed.

"If you have street to street fighting through the rest of Syria, there are going to be hundreds of thousands more refugees pouring out into Lebanon, Jordan, Turkey," Landis said. "And it's going to create a much greater stress on the neighborhood, which could cause their collapse."

The Syrian civil war has already driven more than 3 million refugees to flee across borders into neighboring countries.

7. Stay the course

The White House says the removal of al-Assad from power remains an objective.

"We continue to believe that lasting stability in Syria has to come through a political transition in which Bashar al-Assad leaves power and there is an inclusive governing authority that is formed in that country," a senior Obama administration official said in a briefing Tuesday.

"So long as you have a dictator who is brutalizing his people, you're going to have a much more difficult time reaching the political accommodation inside the country that is necessary for stability," the official said.

But al-Assad has shown no appetite for relinquishing power.

His government has voiced discontent that the airstrikes against ISIS took place without its permission. But officials from the regime have been suggesting for a while that American and Syrian government interests are converging.

Obama "would benefit a lot from cooperating with the Syrian government against terrorism because we have been truly fighting terrorism for the last four years," Bouthaina Shaaban, the political and media adviser to al-Assad, told CNN earlier this month.

With the campaign of airstrikes against ISIS set to go on, U.S. official will continue to be faced with such awkward assertions.