We have it laid out for us, the primary purpose of the flotillas is to force the Israelis hand and hurt their international standing by causing them to act to enforce the flotilla. Never mind the fact that Israel's unilateral withdrawal from Gaza saw a marked increase in rocket fire into Israel and the election of a radical terrorist group to represent the people of Gaza. More interestingly, the freedom flotilla organizers are not taking a stand against Egypt and its apparent about face on opening the Rafah border freely. The flotilla organizer mentions the lack of foreign aid flowing into Gaza through Rafah almost in passing, focusing exclusively on Israel while ignoring the fact that the post-Mubarak Egyptian government promised to lift restrictions on Rafah and allow a freer transit of goods and people from Gaza to Egypt and vice versa (though I am not sure why any Egyptian would want to go to Gaza).
In reality, the Egyptian government reimposed restrictions on Rafah only 3 days after opening the border, and there is rising concern that Hamas and other militants associated with al-Qaida and other groups are moving into the Sinai Peninsula, an area with notoriously low military and police control. To the extent that the Egyptian military still runs and controls the government, there are real concerns that the flow of Islamist militants into Egypt could tip the scales in the Muslim Brotherhood's favor in determining who will control Egypt in the future. There is good reason for the Egyptians to be highly concerned about who is leaving Gaza, but it is less clear why the Egyptians refuse to allow humanitarian aid in. Moreover, one might believe that the Freedom Flotilla organizers would pressure Egypt if they had any interest in resolving the humanitarian crisis in Gaza.
The fact is quite simple: the flotillas are not and have never been about humanitarianism. They are simply about putting Israel into a difficult position and drive international opinion against it. It is difficult for me to imagine how exactly the Israelis can resolve the current Gaza crisis knowing that the government in Gaza (and now the West Bank) contains substantial elements that are explicitly dedicated to its destruction. It is quite easy for the flotilla organizers to delude themselves into believing that Israel can allow a free flow of arms, goods and people into Gaza and that the result will be the creation of some sort of Arab paradise that will no longer have qualms with the Israelis. The 2006 Lebanon War proved exactly what happens when Israel does not act to restrict the flow of arms and goods along its borders. Hezbollah launched its war 6 full years after Israel unilaterally withdrew to the borders that existed in 1978 before Operation Litani. Considering that both Hamas and the PA seek to liberate Palestine "from the river to the sea," asking Israel to remove restrictions on Gaza and the West Bank is asking it to sacrifice civilians to its enemies for nothing.
Since unilateral withdrawals from Gaza and Lebanon failed to bring peace, it is not clear exactly how the freedom flotillas can even accomplish the goal of promoting peace, if that is their goal. Considering the current lack of peace talks, any Israeli action vis-a-vis Gaza or the West Bank must be unilateral by its nature. But, if unilateral withdrawals and unilateral "settlement" building moratoriums have failed to bring reciprocity from the Arabs, then what is their value? If Israel's withdrawal from Gaza was answered with rockets, it is very conceivable that its easing of goods and transit restrictions will be answered with bigger rockets.
The core issue with the flotillas like the Mavi Marmara is that it is difficult at best to determine what their goal is. Since humanitarian aid is not their primary concern since they do not attempt to transport goods through Rafah (I think because they are scared of what the Egyptians will do to them) and the geopolitics of the Middle East preclude unilateral Israeli concessions from bringing about any positive change in Israel's relationship with the Palestinians, one can only see the flotilla organizers as seeking to aid those who seek to destroy Israel wholesale.