The "humanitarian protesters" tried to kidnap three of the Israeli soldiers. Further evidence of weaponry was found:
... After the incident, 9mm bullet casings were found - a kind not used by the naval commandos. The Israel Defense Forces says that during the operation a number of pistols and an M-4 rifle were taken from soldiers, but they believe that the Turkish activists had other weapons. The captain of the ship told the naval commando chief that the guns were thrown overboard before the ship was completely taken over.
There are at least a few honest journalists that challenge the protesters on their version of what happened:
The above from Just Journalism which has an ever growing reputation for unbiased reporting.
Now don't get me wrong. The handing over of Israel by the British many decades ago was probably not in the best interests of the region. But it is done. It can't be undone unless you support another holocaust. So there has to be some way to come to an agreement. But as long as the Palestinians allow Hamas to represent them, there will likely be violence.