[Edit] As Nilgiri has pointed out, it was the Jordanians that killed him. Just replace Israel with Jordan, and my point still makes sense. The Jordanians aren't kind to dark-skinned skinned people, including dark skinned Arabs and Muslims.
One of two possibilities.
He was sympathetic to the Israelis and wanted to live in Israel, and the Israelis shot him because he's a brown guy trying to cross the border.
Or
He was sympathetic to the Palestinians, and wanted to live in Palestine, and the Israelis shot him because he's a brown guy trying to cross the border.
Either way, Israel almost certainly shot him because of his dark skin.