First off, let me begin by saying that Lee didn't want a long, drawn out confrontation at Gettysburg. The reason Lee was roped into battle at Gettysburg is more because of the lack of control in his army and among his subordinates opposed to his tactics. One of the most important things to note for the Confederates at Gettysburg is that the battle began without the presence of J.E.B. Stuart, a famous cavalry officer in the Confederate army.

Stuart had embarked upon a "wild ride" shortly before the outbreak of battle, in what most consider an effort to display his distaste for the Union and its troops. Stuart was a gifted tactical commander, but a notorious wildcard. Without him present during the first day and second morning of battle, Lee was at a significant disadvantage. Secondly, it's worth noting that Stuart had a number of missions to complete on this jaunt of his... which he prioritized over returning to battle with Lee.

In this regard, you can identify that Stuart did not in fact take an unauthorized jaunt, but did take his own orders over that of Lee's-- both of which were in admittedly bad timing.

Back to the point, another example of this lack of control was evident when General Longstreet failed to break into Union Lines during an assault on Day 2 of the battle, because of "tardiness in action."

It's said that Lee and Longstreet had a disagreement over whether or not to attack the line, with Lee citing vulnerabilities in the line and Longstreet vehemently objecting to the assault. In the end, Longstreet DID attack... several hours late, when the line had been fortified. Obviously, this did not go well.

To answer your question, finally and directly, Lee was still held in high regard because Lee was not directly blamed for these failings. His tactics, had they been faithfully and dutifully executed, would have likely been enough to either avoid the engagement (I've heard an infantry unit scouted Gettysburg instead of a Cavalry unit, which Lee also objected to) or manage a win over Union forces. It's because of Lee's tactical ability, thinking capability, and charisma that he is considered a great general in the first place.

As the saying goes, "you don't blame the man with charisma, he blames you."

why did Napoleon's troops love him after Russia and Leipzig? one battle does not destroy a reputation such as the one Lee built.

The post war "soldier's peace," Lee's post war apolitical role and Longstreet's republicanism (opening himself up to unfair criticism by the virginia school) helped post war romanticism of people's own (and the collective) view of Lee as well

First, Lee's loss at Gettysburg was while leading a veteran army that had performed consistently well for 2 years, often against poor odds. Given that the Union was unable to pursue, it's not unreasonable that The army still had faith in their general.

That said, even if you were unhappy with Lee, what are your other alternatives? By the end of Gettysburg, the Confederacy was awfully short of able corps commanders, much less army commanders.

Many contributors have made excellent points. sunday_silence is right on in his assessment. I would like to contribute another point with some sources. According to S.E. Woodworth, Jefferson Davis' sense of honor, personal commitment to those he trusted, distrust of everyone else, and sense of his own military prowess--in essence his personality quirks--were at the root of his relationships with every general in Confederate service. In the last analysis, Davis trusted Lee and short of an outright revolt of the entire army (which is probably the only reason he removed Bragg in the West) Davis would never remove Lee. Also add to the fact--as others pointed out--that the CSA leadership was degraded to the point were officers capable of leading a sophisticated army was minimal at best. AND those politically connected enough and in Davis' circle was even smaller. In short, Lee was all they had in the East. Proof of this is the CSA's conduct in the West, were they were essentially outclassed (leadership wise) from late 1862 onward.

Sources: Woodworth, Steven E. Jefferson Davis and His Generals: The Failure of Confederate Command in the West. University Press of Kansas, 1990.

Gallagher, Gary W. Lee and his generals in war and memory. LSU Press, 1998.