It was the largest single loss to the US intelligence community in history. Based on the interviews conducted with the survivors I don't believe that it was an accident. I don't know why exactly Israel would choose to attack a US flagged ship. I do believe that it was politically expedient for both the US and Israel to chose to ignore the whole thing.
Israel looks out for Israel. There's no reason the US shouldn't be doing the same. Basing our foreign policy on what benefits another nation is foolish in the extreme.