President Barack Obama clashed so often and so publicly with Israeli Prime Minister Benjamin Netanyahu during the first 16 months of his tenure that one Israeli newspaper reported Netanyahu believed Obama wanted a confrontation to improve U.S. ties to the Arab world.

Then on May 31 came a moment that former U.S. Ambassador Martin Indyk says showed the real nature of Obama’s policy toward Israel: the deadly raid on an aid flotilla bound for Gaza that unleashed a torrent of international criticism and a move in the United Nations to censure the Jewish state.

Obama responded by siding with Israel, shielding it from direct condemnation by the UN Security Council. In doing so, analysts including Indyk said, Obama showed he embraces the core policy of predecessors Bill Clinton and George W. Bush: The U.S. will give Israel unwavering diplomatic and military support even as tensions test their relationship.

“At the end of the day, what every president and prime minister have come around to realizing is a fundamental truth: both countries need each other and they have to find ways of working together,” said Indyk, who served as U.S. ambassador to Israel for Clinton and during Bush’s first six months and is now a senior fellow at Washington’s Brookings Institution.

In the last few months, the U.S. and Israel have butted heads over settlements, their leaders haven’t appeared publicly together, and Israel’s flotilla raid frayed U.S. ties to Turkey, an important ally.

An especially strained moment came in March, when Israel announced it would build 1,600 homes in East Jerusalem, an area claimed by Palestinians, during a visit by Vice President Joe Biden. The move delayed indirect Israeli-Palestinian peace talks that the U.S. has brokered and drew a reprimand from Secretary of State Hillary Clinton.

Shortly afterward, Netanyahu met with Obama at the White House. They made no public appearance together, as is customary when a foreign leader visits.

Even earlier, Obama had put Israel and its supporters on edge when he went to Cairo in June 2009 to call for a “new beginning” between the U.S. and the Muslim world.

It was the Cairo speech that prompted Netanyahu’s suspicion Obama was seeking a clash with Israel to bolster Arab ties, Haaretz reported on June 9, 2009, citing unidentified confidants of the prime minister.

The Obama administration, unlike its predecessors, “made a very public display on the settlements,” Israel’s ambassador to the U.S., Michael Oren, said in an interview. Because Netanyahu leads a “center-right government,” he said, “the pushback was greater than it had been maybe under a leftist government.”

Still, the relationship “hasn’t changed that much,” Oren said.

“We have an extremely close relationship with Israel,” said White House spokesman Tommy Vietor. “Israel’s a friend, sometimes friends disagree.”

Palestinians are disappointed by what they see as Obama’s shift toward Israel, said Mkhaimar Abusada, a political scientist at Al-Azhar University in Gaza City, in a telephone interview.

“The high hopes we had for the Obama administration have evaporated,” Abusada said. “He seems to have collided with the other institutions in American politics and cannot apply the pressure on Israel that is needed to stop settlements and push the peace process forward.”

The strategic alliance has survived its challenges in large part because of mutual need, said Ziad Asali, president of the Washington-based American Task Force on Palestine, which according to its website works to promote a negotiated peace settlement giving Palestinians their own state.

“The warmth and friendship between the president of the U.S. and the prime minister is not there anymore, but the relationship is sound and solid,” Asali said. “The U.S. and Israel have too many things in common and too long a history of strategic relations to be seriously impacted by political differences.”

The Obama administration must maintain strong ties to Israel to move forward on Israeli-Palestinian peace talks, which are important for improving U.S. ties to the Muslim world, said Asali and David Makovsky, a senior fellow at the Washington Institute for Near East Policy. The allies also are in sync facing the threat of a nuclear Iran.

While tensions are a natural part of the relationship, the two nations always settle into the “abiding reality” that they must work together, Indyk said.

After the flotilla raid and the deaths of nine activists aboard, the U.S. followed up its protection of Israel from denunciation by name at the UN by working to put together an inquiry into the event that will both satisfy world opinion and buffer Israel, Makovsky said. Obama and Netanyahu spoke three times in one day during the crisis, he said.

It wasn’t the first time the Obama administration had followed such a course.

In November, it opposed a UN report that accused both Israel and Hamas of war crimes during a three-week conflict in Gaza that ended in January 2009. Israel, the U.S. and the European Union consider Hamas a terrorist organization.

In October, the U.S. withdrew from joint military exercises with Turkey when it barred Israel from participating. And the U.S. continues to assist Israel with military support and missile defense, Daniel Benjamin, State Department coordinator for counterterrorism, told a Senate committee on June 8.

The U.S. has helped Israel with David’s Sling, a system meant to counter medium-range rockets that is scheduled to be operational in 2012 or 2013. And in May, the administration announced Obama would seek $205 million for a medium-range missile defense system for Israel called Iron Dome.

“Our efforts will help ensure that Israel maintains the capability to defend against and mitigate these threats,” Benjamin said.

The Obama policy bears the hallmarks of the approach that both Clinton and Bush took.

Clinton clashed with Netanyahu over the Israeli leader’s settlement expansion program that Clinton said was delaying the Middle East peace process. Still, he poured political capital into those talks, oversaw the signing of a Jordan-Israeli peace treaty and maintained steady military support for Israel. In 1996, he offered $100 million for Israel’s anti-terror activities and another $200 million for the Arrow anti-missile deployment system.

Bush sparred with then-Prime Minister Ariel Sharon over Sharon’s October 2001 comment that the U.S. was appeasing Palestinians to win Arab support for its war on terror, which Bush called “unacceptable.” Later that month, Israel rejected a U.S. call to withdraw immediately from Palestinian-controlled areas in the West Bank.

Still, Bush continued military support and gave Israel $9 billion in conditional loan guarantees in 2003 after a Palestinian uprising and an economic slump in Israel.

And Bush didn’t repeat Clinton’s criticism of settlement activity, telling Sharon in an April 2004 letter that any final Israeli-Palestinian settlement must take into account changed “realities on the ground, including already existing major Israeli population centers.”

Even earlier, under President Ronald Reagan, the U.S.- Israeli relationship had rough patches. In 1981, the U.S. voted with other members of the UN Security Council to condemn Israel’s bombing of Iraq’s Osirik nuclear reactor. A year later, Reagan supported Israel’s invasion of Lebanon.

Remaining Israel’s defender serves several U.S. strategic goals, Makovsky said.

“If the U.S. doesn’t have a close relationship with Israel, it will be harder, not easier, to get it to withdraw from certain territories in the West Bank because an Israel that is not secure will not take risks for peace,” he said.