Erdogan is a repulsive anti-Semite, and apologizing to him because soldiers defended their own lives against violent rioters masquerading as "activists" angers me.
But I don't think that Netanyahu would have done this for no reason, or just because he was pleased by Obama's visit.
The following is speculation.
I notice that the "reconciliation" happened very late in the visit, but that it was far from spontaneous; the diplomatic push began 2 weeks ago, purportedly triggered by a letter that 89 senators sent to Erdogan after his recent anti-Semitic rant:
On March 12, 89 members of the U.S. Congress wrote a letter to Erdoğan and asked him to retract his words on Zionism, which he did not; he said he stood behind what he said but he had been misunderstood.
It seems that letter triggered the U.S. move, since the White House wanted to see its two main allies in the region work together once again as they did until the “one minute” incident in Davos in 2009.
Turkey's foreign minister said:
I spoke with Kerry six times over the last week. We talked about the negotiations on the texts [of the apology]," he said. Davutoğlu noted that during the last week Turkey had only been in contact with U.S. officials, who mediated the final agreement before U.S. President Barack Obama's Israel visit. "We agreed that [Israeli Prime Minister Benjamin] Netanyahu would call the Turkish prime minister accompanied by President Obama. Each word of the agreement has been studied. We worked on it until the morning and at noon we got a clearer picture."
Erdogan appears to have sought the approval of Hamas and Fatah before he accepted the call - which speaks volumes. Turks may well ask who is the final arbiter of Turkish foreign policy. But I won't go off on that tangent. Hurriyet:
Davutoğlu also said that Prime Minister Recep Tayyip Erdoğan called both the Hamas prime minister of Gaza and the leader of the Palestinian Authority to get their approval before accepting Israel's formal apology for the Mavi Marmara raid. He explained that the conversations took place moments before Netanyahu's call. He added that Erdoğan also called Egyptian President Mohamed Morsi and Lebanese Prime Minister Najib Mikati. "The tripartite meeting started afterward. Netanyahu began, then passed the phone to Obama. [Other sources say that it was the other way around - Zvi] I did not count the minutes, but the call lasted between 20 and 30 minutes," Davutoğlu said.
The "reconciliation" was evidently an important objective of the visit, but this has not really been acknowledged. For most of the visit, the press babbled on about the Palestinians and all but ignored Israel-Turkish relations. Even afterward, Obama almost seems to be deemphasizing the Israeli-Turkish meeting, though he is clearly pleased with it.
Which leaves me thinking about Syria, and about Iran.
In Jordan, after leaving Israel, Obama said, "I am very concerned about Syria becoming an enclave for extremism because extremists thrive in chaos, they thrive in failed states, they thrive in power vacuums."
The situation in Syria is going critical. Israel, Jordan and Turkey are Syria's neighbors. Chemical weapons are being used by the regime, and maybe by some of the rebel groups. Did Obama tell Netanyahu that a new phase has arrived, and that the only way to prevent the spread of chemical weapons among al-Nusra (closely aligned with al Qaeda in Iraq), and throughout the failed Syrian state and the region, is for Israel to work together very closely with Turkey, at the highest levels? I don't know.
Netanyahu has always been a pragmatist. He has never been the strongest-willed leader, but he does try hard to save Israeli lives. I can easily imagine him agreeing to the lesser of two evils - a formula that includes an apology for any mistakes made, as long as the soldiers are protected from revenge harassment by the Turkish state - if it might achieve something that is far more important. I can easily imagine that with really solid US guarantees, he would have been willing to pick his battles and set aside the fight with Erdogan in order to save thousands of Israeli lives.
In Jordan, Obama also indicated that he would ask Congress to provide more budget support for the kingdom, which currently houses 460,000 Syrian refugees. This is consistent with a deep concern in Washington about the civil war raging in Syria, especially if one expects the situation to grow much worse before it improves.
After meeting with the Jordanians, John Kerry will return to Israel. But he won't return to Ramallah. The president's conversation with King Abdullah concerns Syria at least as much as it concerns the Palestinians, and probably much more.
At the same time, Turkey is reaching out to the Kurds, and Abdullah Ocalan has responded.
Things are shifting in the region, some of them below the radar, and I think that meltdown of Syria lies very close to the center.
And then there is Iran.
Turkey's subsequent behavior will tell us a lot about the strategic importance of this "reconciliation." If Erdogan demonstrably ends his attacks on Israel and actively promotes cooperation, then that will tell me that Turkey views reconciliation as strategically vital. If not, then Erdogan's regime views all of this as a "political football," all speculation aside.
Bülent Yildirim of the IHH claims that the trials of the Israeli soldiers in the ICC will go ahead; but this is apparently incorrect.
Sometimes, when the risk of fire is high, you need to establish firebreaks that can prevent a conflagration from getting out of control. Obama and Netanyahu both know this. Erdogan may be thinking along the same lines.
UPDATE: See also The Daily Beast. And Foreign Affairs.