Despite the call for unity, Petraeus is taking over an increasingly divisive war strategy.
He is the architect of the counter-insurgency doctrine the US is now applying in Afghanistan. It emphasises protecting civilians and improving governance over killing fighters.
The Taliban timed an attack on a US aid contractor to coincide with Petraeus' arrival
The strategy has strong support at the highest levels of the military, but it receives mixed reviews from rank-and-file soldiers. Some think it limits their ability to defend themselves.
The Rolling Stone article published last week that led to General Stanley McChrystal's sacking depicted a number of soldiers questioning the counter-insurgency strategy.
"During the question-and-answer period, the frustration boils over," wrote the article's author, Michael Hastings, describing McChrystal's visit to an outpost near Kandahar. "The soldiers complain about not being allowed to use lethal force, about watching insurgents they detain be freed for lack of evidence."
Petraeus said at his senate confirmation hearing that he would review the rules of engagement, but suggested those changes would be minor - easing bureaucratic restrictions, not rewriting the rules of war.
Some Afghans, too, have called for Petraeus to rethink US strategy.
Ahmad Behzad, a parliamentarian from the western province of Herat - and a longtime critic of Hamid Karzai, the Afghan president - said after Petraeus' remarks on Saturday that the new general should take a harder line against the Taliban.
"Petraeus must change the fundamental strategy of the war against the Taliban," Beshad said. "A change in the leadership of foreign forces can only be effective if we see more serious steps taken against terrorists."
Other divisive issues continue to loom over the war effort in Afghanistan. Despite Saturday's public display of unity - Petraeus appeared at the embassy with Karl Eikenberry, the US ambasasdor to Afghanistan - it's unclear whether the two men will work together effectively. McChrystal and Eikenberry were reported to have had a frosty relationship.
Eikenberry opposed the plan to send more US troops to Afghanistan [AFP]
US and Nato officials are still vague about their planned autumn campaign against the Taliban in the southern province of Kandahar. The campaign was initially dubbed a "military offensive" but has since been scaled down, and commanders now vaguely call it a "concept".
But the plan - whatever it is - is still deeply unpopular with Kandahar's residents, a majority of whom say they do not want a major operation in their backyards.
The war continues to create deep divisions among the US public too. A June 24 Newsweek poll found that 53 per cent of Americans disapprove of the handling of the war by Barack Obama, the US president, up from just 27 per cent in a similar poll in February.
A June 6 Washington Post poll found that a majority of Americans - 53 per cent - do not think the war is worth fighting.
Senator Carl Levin, the head of the US senate's armed services committee, said earlier this week that US support for the war "will depend on this fall in Kandahar".