The short answer is that Robert E. Lee became a hardcore Confederate nationalist, but the story of how that came to be is very interesting.

Antebellum Americans weren't just loyal to their states OR the nation; everyone has a wide variety of loyalties, which wax and wane according to circumstance. Beyond state loyalties, they were often conscious of being part of a region or section, and after secession, they expressed loyalty not just to their section but to a new nation.

For many years, Lee's most important loyalty was to the nation. His father had fought under Washington in the Revolution, and Washington, the prototypical American nationalist, was his idol throughout his life. His family had a generally Whiggish (broadly, the party of moderation and compromise) disposition, and Federalist roots. His father was a strong follower of Washington, and wanted nothing to do with the states' rights Virginia and Kentucky Resolutions of Madison and Jefferson; to him, the Constitution was an act of the entire nation.

He served for thirty two years in the U.S. Army as an engineer, and emerged as the most brilliant soldier of his generation in the opinion of Winfield Scott, himself one of the greatest soldiers in American history. He won some magnificent laurels fighting in Mexico with Scott, and served as Superintendent at the United States Military Academy. He served as the second in command of the 2nd U.S. Cavalry Regiment under Albert Sidney Johnston (Lee was probably more qualified, but as Winfield Scott's golden boy, Secretary of War Jefferson Davis yes that one picked his own favorite for command; Davis held a grudge against Scott because his force received reinforcements while Davis was fighting in the Battle of Buena Vista). When Lee wrote to Winfield Scott upon his resignation, he related the hardship it had taken him to separate himself from 'the service to which I have given all the best years of my life and all the ability I possess.'

Obviously, that's not all there is to Lee. While he was obviously a proud American, he also displayed firm feelings on behalf of the South and its defining institution, slavery. Writing in 1856, Lee responded to a speech by President-Elect James Buchanan.

" I was much pleased the with President's message. His views of the systematic and progressive efforts of certain people at the North to interfere with and change the domestic institutions of the South are truthfully and faithfully expressed. The consequences of their plans and purposes are also clearly set forth. These people must be aware that their object is both unlawful and foreign to them and to their duty, and that this institution, for which they are irresponsible and non-accountable, can only be changed by them through the agency of a civil and servile war."

Lee had supported Buchanan because he wasn't an extremist; he wasn't a radical Southern Fire-Eater, nor was he an Abolitionist. There would be no threat to the South's domestic institutions [slavery] while Buchanan was president; while he referred to extremists in the North and the South together, the letter identifies which threat he sees as paramount. He used a fairly common stereotype of New Englanders (then the heart of the radical abolitionist movement) to contrast with his Southern conservatism.

"Is it not strange that the descendants of those Pilgrim Fathers who crossed the Atlantic to preserve their own freedom have always proved the most intolerant of the spiritual liberty of others?"

Things become very conflicted during the winter of 1860-61, during the secession crisis. In the election of 1860, there were four candidates, and one issue that people really cared about: Would slavery be allowed to expand into the territories acquired in the Mexican War? The Republican candidate, Lincoln, wanted that land exclusively for white, smallholding citizen-farmers, and to forbid slavery in the territories. The Democrats split into two factions. The Northern Democrats, led by Steven Douglas, wanted to allow the people of the territories to decide for themselves whether slaver would be allowed. In contrast, the Southern Democrats, choosing Vice President John C. Breckinridge to run; they demanded a 'Federal Slave Code', basically allowing slavery everywhere it isn't specifically banned by state. Although he opposed it as a solution, it was widely known that Breckinridge believed in the right of secession. The last party was the Constitutional Union Party, which ran John Bell. They wanted to extend the Missouri Compromise line to the Pacific Ocean, and guarantee slavery forever south of the line as a compromise to preserve the Union as it was forever.

Lee is in Texas when the election transpires. Nobody in Texas votes for Lincoln, and not many more for Douglas. The real competition was between Breckinridge and Bell, and this actually surprised me a bit. In Virginia, the wealthy, slaveowning counties generally went for John Bell, but in Texas, Lee wanted Douglas to withdraw from the race and throw his support behind Breckinridge so they could stop Lincoln. It was widely believed that if Breckinridge lost, the Southern states should secede from the Union, but while he supported Breckinridge, before April of 1861, Lee still denies the right of secession. Breckinridge won most of the South, excepting Virginia, Kentucky, Missouri, and Tennessee, and four days after Lincoln's victory, South Carolina called for a convention on secession. In this initial period, there was some support for just letting the South go. Winfield Scott wasn't a secessionist, but he didn't want to prevent it through military force or punish those who seceded, and Horace Greeley didn't want to keep one section of the country pinned to the other by the point of a bayonet.

At this moment, Lee was considering two alternatives. If the Union was dissolved peacefully, he'd head back to Virginia once the Department of Texas was withdrawn or disbanded. If, however, the administration determined to fight the dissolution of the Union, he was still willing to join them; he considered it a great opportunity to advance his career.

"If the Union is dissolved, which God in his mercy forbid, I shall return to you. If not, tell my friends to give me all the promotion they can."

Robert E. Lee, Dec 5, 1860.