"We know you're monitoring us, fuck off and stop or this will happen again."
The US was not wholly in Israel's corner at the time - the very early state of Israeli interference in US politics meant that there was still a strong pro-Arab strain in US foreign policy. It may have been legitimate suspicion that we may have been passing intel along, or it may have just been a "If you aren't with us, you're against us" message to ward any US involvement in the conflict without Israeli approval.
It's extremely hard to believe that they launched multiple sorties on a plainly identified US ship and had it all attributed to the error of multiple pilots and naval crew, who all conveniently believed the the US flag-waving ship in international waters was actually an Egyptian destroyer.