Hundred of activists were on the flotilla. So a few were part of groups that Israel doesn't like. That doesn't change whether the siege of Gaza is legitimate or whether killing the activists on the board the boat is any less murderous. Were the Hamas guys the ones that died? I doubt it. If the IDF could show that it shot Hamas men, it would be trumpeting that as justification for its murders.
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from the article: IDF: Five Gaza flotilla activists linked to Hamas, Al-Qaida