/u/TRB1783 covered this question in an answer of theirs. The long and the short of it is that the popular image of Lee embodied a set of attitudes that made him quite popular in defeat. Much of his legend is embellished in the post-Reconstruction period where he became a gallant symbol of a sanitized Confederacy.
Why isn't Albert Sidney Johnston held in the same regard as Lee?
I'm going to be more anecdotal in this answer than I would normally be as I grew up in Lexington, VA where Robert E Lee lived out his retirement as the President of a small liberal arts college which is, today, Washington and Lee University.
Lexington is/was home to both Lee and Jackson and, growing up there, it's impossible to escape the mythos of both men. The best answer I can give you is that - if you look at history as a story that's told rather than an academic discipline - Jackson and Lee are among the most compelling and relatable characters of the war.
Lee and Jackson fight for the historical underdog. Now, yes, our modern perspective on the war puts the South clearly in the "bad guy" role but they were clearly and unambiguously the plucky underdogs facing down the larger more powerful North. Underdogs make for good story telling.
Lee and Jackson were gentlemen. Aristocratic Lee much moreso than the orphan Jackson (orphans are also good storytelling fodder) but nonetheless both held to notions of propriety, faith, and culture to which many still aspire today.
Both were brilliant in their own right but in a 19th century Napoleonic "war as romantic struggle" sort of fashion rather than, as became the case late in the war -- the 20th century "war as mechanized horror" manner. Sherman and Grant were every bit Lee and Jackson's equals in that capacity, but the kind of war they excelled at is one that we find distasteful.
Finally, they were white-washed of the more troublesome racial overtones of the war. The civil war was unambigiously about slavery (and anyone who tells you otherwise is selling something) but Lee's hesitancy to lead the Southern Armies and Jackson's peculiar views on slavery and slave laws make them far more palatable figures than some of their more cartoonishly racist contemporaries.
These qualities were among those capitialized upon by the post-war PR campaign mentioned by /u/TRB1783 in the comment linked by /u/kieslowskifan