But some Bush administration officials fear the militias could steer Somalia toward Taliban-style Islamic fundamentalism.
"[Our] first concern, of course, would be to make sure that Somalia does not become an al-Qaida safe haven, doesn't become a place from which terrorists plot and plan," President Bush said after learning of the Islamic militias' takeover in the capital.
Analysts watching developments in Somalia, and Somali expatriates, claim the U.S. fear of a fundamentalist regime in a country known for its moderate religious beliefs is unfounded.
"I'm not too concerned that [the Islamic courts] will be able to impose the kind of draconian rules that the Talibans or anybody of that ilk have done to their people," said Abdi Samatar, a geography professor at the University of Minnesota who was born in Somalia, said on the June 6 NewsHour with Jim Lehrer.
"What's relatively very refreshing about this group is the fact that they have committed themselves to say that they are not interested in becoming ministers; they are not interested in becoming government, but what they want to do is create the conditions in which the Somali people ... could be able to have determination as to which way they want to go," Samatar said.
The Islamic court system, under which the militias fighting in Mogadishu operate, emerged in the 1990s after rebel warlords seeking to depose former dictator Mohamed Said Bare descended into infighting in the capital and elsewhere. With no national police force to impose law, the warlords turned to the Islamic courts for stability, according to Lee Cassanelli, an historian and Somalia expert at the University of Pennsylvania.
Empowered by clan leaders and the warlords now fighting them, the courts helped resolve disputes within clans, in some cases using Sharia law to execute criminals and cut off the limbs of petty thieves. The clans and warlords provided the courts with armed militias to help enforce their decisions.
"They were vehicles for drawing on the Islamic sheikhs to help mediate internal disputes," said Cassanelli. "Some of them acquired a prestige and respect among the populous because they were seen to be outside of the petty fighting."
In 2000, the courts formed a union of Islamic courts, partly to consolidate resources and power and partly to aid in handing down decisions across, rather than within, clan lines.
Since then, the Islamic Courts Union has come to be seen among Somalia's citizens as the provider of daily services in a continually unstable country.
"The thing that makes the Islamic courts very popular, the areas they control you can walk at night," said one Somali-American, who declined to give his name for fear of reprisals against his family back home. "The areas the warlords control, you can't walk. You can't carry a mobile phone; they'd take it from you. They even can rob you and kill you."
According to diplomats and analysts, the Islamic courts are responsible for the few schools that are open in the capital as well as some hospitals.
Despite this, according to Cassanelli, the United States still does not trust the Islamic Courts Union. "We think they are breeding grounds for terrorists," he said.
Many Somalis are convinced that the CIA has been funding the warlords in their fight against the militias, further boosting support for the Islamic courts because of a growing anti-U.S. sentiment.
Former Clinton administration official John Prendergast, who analyzes Somalia and other African countries for the International Crisis Group, told Reuters evidence suggests the CIA is providing the warlords with up to $150,000 a month in supplies. Others claim the Ethiopian government, working in tandem with the United States across the border, also is sending in truckloads of arms.
While the State Department has neither denied nor admitted to backing the warlords, some officials claim Somali Islamists could be harboring terrorists and blame bombings across the border in Kenya on efforts launched in Mogadishu.
Two militants associated with the courts, Sheikh Hassan Dahir Aweys and Adan Hashi Ayro, have been accused of heading militias linked to al-Qaida and of carrying out murders against Somali citizens and foreign nationals including BBC producer Kate Peyton, the BBC reported.
"There are no fugitives from al-Qaida or any other organization, as the U.S. and Ethiopian intelligence services are claiming, Sheikh Sharif Ahmed, head of the Islamic Courts Union, said in an interview with the Arab daily news service Asharq Alawsat in May.
In June, Ahmed told the BBC's Arabic news service the courts symbolize a "revolution by the Somali people after 16 years of anarchy and killing, plunder and kidnapping."
"This body is not a political one. Rather we want to give power back to the Somali people so it can make its own decisions and decide its own destiny," he said.
Ahmed, who emerged in the late 1990s as a neutral mediator respected by many of Somalia's clans and now seen as a hardliner by Western governments, was appointed head of the Union at its formation and now serves as its chief spokesman.
While he has promised not to steer the country in a fundamentalist direction and to refrain from seeking a post in the government, only time and talks between the Union and the largely ineffective transitional government serving in exile outside the capital, will tell.
"The best resolution that I could see that could work is if the Islamic courts talk to the government, the government comes to Mogadishu and the fear of the American government's involvement is lifted," the Somali expatriate, who did not want to be named, said.
The international community also should step in and take advantage of the lull in violence and the recapture of Mogadishu to help the Somali people, said Samatar.
"[The Islamic Courts] want to invite all the international community to come to Mogadishu and look at every cranny and nook to be able to see if there are terrorists. ... I think we call their bluff and call them on their word," he said.
Cassanelli, who has studied Somalia for 30 years, said he is not as worried as some in the State Department about terrorists taking hold in Somalia and the country turning to religious extremism.
"Somalians are very pragmatic people ... there wasn't this huge new wave of Islamist sentiment, people were just getting fed up with the warlords. Anything's got to be better."