It boils down to motivations and one's sense of "honor." Let's start off with what each of them actually did.

Benedict Arnold was quickly becoming one of the most valuable generals in the Continental Army. He had repeatedly proven to be an able and useful commander. Long story short, he used his pull to get put in charge of West Point (an extremely important fortification at the time) and tried to hand it over to foreign army. Even if you don't want to consider the British as "foreign," it was an extremely dishonorable act. If at the beginning of the war he had declared loyalty to the British and fought as a British general, we likely would not feel the same way about him today.

Lee, on the other hand, had fought for the United States for 32 years before the civil war, and tried as hard as he could to avoid fighting for either side. Here are some good quotes of his :

"I shall never bear arms against the Union, but it may be necessary for me to carry a musket in the defense of my native state, Virginia, in which case I shall not prove recreant to my duty."

When asked to lead the Union army, his response was this:

"Mr. Blair (Presidential Adviser Francis Blair), I look upon secession as anarchy. If I owned the four millions of slaves in the South I would sacrifice them all to the Union; but how can I draw my sword upon Virginia, my native state?"

He didn't want the war, but he couldn't raise his hand against his home state, his family, his neighbors. It was a difficult choice, and by most accounts he was an admirable man (as admirable as a slave owner can be anyway). He was essentially forced to choose between his "nation" and his home. This was a choice everyone in the south had to make, and it weighed heavily on Lee. It's also part of why leniency was given to those who took up arms against the Union.

It's important to remember at this time someone from Alabama had likely not ever even left the state, let alone met someone from New York. The Union states were as foreign to the average Confederate soldier as Canada would be. (This does not exactly apply to Lee, in his long military career he had been all over the country, he was coincidentally Superintendent at West Point for a time, the same fort Arnold tried to sell to the British. It was now the Military Academy.)

Fighting for the south was specifically pardoned by President Johnson in 1868 as part of extending the olive branch after the war. Jefferson Davis was actually imprisoned for treason but was later released.

At the end of the day, the north had to reconcile with the south for there to ever be a strong union again. Hanging war heroes (to the southerners, and a few northern admirers) would do nothing but breed animosity in those who were already bitter from defeat and reconstruction.

I also wouldn't really say Benedict Arnold is propped up or inflated for his treason. What he attempted is one of the most deceitful, dishonest, and damaging things a person could do in his lifetime. Even the British did not respect him. Here's a good quote about his reception back in England:

In London, he aligned himself with the Tories, advising Germain and King George III to renew the fight against the Americans. In the House of Commons, Edmund Burke expressed the hope that the government would not put Arnold "at the head of a part of a British army" lest "the sentiments of true honor, which every British officer [holds] dearer than life, should be afflicted.

Even the British made jabs at his lack of honor. Lee, and many of the confederate soldiers could justify their crimes as defending their homes once the states had seceded.

The argument then shifts to the politicians that seceded. While it could be reasonable to expect them to be punished, the north was very keen on rebuilding a strong union as soon as possible. Starting a witch-hunt to track down secessionists could have easily destroyed any goodwill they had gained with their pardoning of soldiers. It was decided that it was best if everyone put the animosity behind them to work on building a strong, united country. There was a very strong movement to punish the south for the war, but cooler heads ended up prevailing.

Lee was almost like the "reluctant rebel." This was a time where we really gave a shit about our states. This was an era, which we can never know, where states had MUCH autonomy, and to impose or encroach on this was considered heinous.