An Aljazeera reporter said that he hard an organizer on the ship say it happened, but this was after Israel fired weaponry on the ships, killed people before even boarding and shot people from above, and the Turks who are not cowards, but were being foolish took iron bars from the ship and attacked in an angry way the Israelis. Israelis would have done the same if fired upon, I suspect. Then, three commandos were taken below, and the organizers said to release them as that would bring more trouble. So, they were released.
Protests in southern Syrian city after Druze cleric's death (AP)
from the article: Israel Navy: 3 commandos nearly taken hostage in Gaza flotilla raid