(sigh)
How many times do we need to go through this?
The "Liberty" was intentionally attacked--because it was believed to have been an Egyptian ship. It shouldn't have been attacked; israel could have known it was an American ship; it could have known that, in retrospect, given the intelligence information it had; but it didn't, due to fog of war and other military SNAFUS.
The definitive investigation of the incident is found in the history periodical "Azure" (unfortunately, only in hebrew). Essentially, it proves that, yes, israeli intelligence DID know it was an American ship... but due to a combinations of foul-ups, simple inattention, and inevitable "time gap" in communications up from intelligence to the high command and back down again to the air force, THIS INFORMATION NEVER REACHED THE AIR FORCE PLANNING DIVISION IN TIME.
Simply put, while intelligence ALREADY knew it was an American ship, the air force STILL didn't know that fact when it sent out the planes to attack what (to them) was an Egyptian ship. That's all there is to it--a tragic delay in relaying information, hardly the first in the history of warfare, I might add. No conspiracy, "coverup", or nefarious world-spanning, high-level pressure was at play.
This sort of thing happens in EVERY war, ALL the time. American soldiers were mistakenly shot at and killed by allied troops--and vice versa--in just about every war the US was involved with. Only recently, the US in Yugoslavia bombed the Chinese embassy and a red cross train--two targets which they should have known very well were there and were noncombatants. In the second gulf war, only a couple of months ago, one allied plane bombed a column of allied soldiers by mistake. These thing happen.
The "it was a deliberate coverup" story is simply an anti-israeli (tras.: antisemitic) conspiracy theory. First, it makes no sense at all: we are supposed to believe that israel, engaged in a three-front war against an enemy outnumbering it 50 to 1, suddenly decided to deliberately attack and kill a ship by its only ally in the world.
Second, the "they didn't want the US to discover what they are doing" story also doesn't hold water: can you think of anything that would make the US MORE interested in what the USS Liberty had discovered than deliberately bombing it? It's like trying to make A ignore B by blowing up B in A's presence. Not a good idea.
Finally, the "they pressured Johnson to cover it up" conspiracy theory (as usual) is self-contradictory. It assumes that israel (or, more accurately, the jews) is both all-powerful and totally powerless.
On the one hand, it assumes that israel was so controlled by the US, that it just HAD to bomb the USS Liberty so that American pressure against israel's "nefarious plans" will not start--the assumption being that the moment the US wants something, israel must do it.
On the other hand, it assumes that israel controls the US so strongly, that it forced a sitting president to ignore and hide proof of its deliverate attack on US seamen--the assumption now being that the moment israel wants something, the US must do it.
Make up your mind! It can hardly be both...
Like all good conspiracy theories, however, it is impossible to show the "true believer" that it makes no sense. It has its "good guys" (the Arabs and the brave souls who discovered "the truth" about the attack on the USS Liberty), its "innocent sheep mislead by propaganda" (most Americans), and its villains (israel, and more generally, the "zionists"--that is, the jews). You cannot argue logically with such an emotionally satisfying picture of the world.
Certainly, I can't; I'm one of THEM, dear true believer, so I am obviously just part of the conspiracy to cover up "the truth"(TM), of course. What can you expect from a jew, after all. But to those of you not already wedded to the "israel is Satan" idea, I hope these facts explain something.