Marvel's one of the most patriotic heroes in comics, but that doesn't mean he obeys every government order without question; this trait was most memorably seen in 2007's Civil War, but has a disturbing precedent set years ago. Steve Rogers is loyal to America's ideas and ideals, not necessarily to America itself, and that extends to American politicians. When push comes to shove, he will even actively disobey direct orders - and in Avengers #63, even inspire others to do the same.
In Civil War, a disastrous battle involving the New Warriors team prompts the United States to enforce the Superhuman Registration Act: legislation which promises to heavily regulate all superhuman activities and force superheroes to reveal their secret identities to the government. While some like Iron Man think the SRA is necessary for the superhero community and the world at large, Captain America sharply disagrees, believing the legislation is too vague and infringes on too many individual freedoms. As Civil War plays out, Captain America fights against his own government, and what is a shocking development for some was foreshadowed many years ago.
In Avengers #63 in 1998, a protracted battle between Thor and Iron Man leads the United States Army to mobilize and send in ground forces (and the situation isn't helped by Russian bombers ready to attack the area). Captain America finds himself surrounded by soldiers sent directly from the President of the United States, and tells the group to hold their ground and not advance. Captain America is not the ranking officer present - but he's still Captain America, and this prompts every soldier to salute Rogers and obey his orders instead of the President's own.
In simple , Captain America has just committed a coup by ordering soldiers to disregard the President's orders as Commander-in-Chief. This behavior is tantamount to treason, and as Captain America is still in the US Army as a captain, subject to incredibly harsh punishment under the UCMJ. If Steve Rogers was willing to do this nearly ten years before Civil War, no one ought to be surprised when he turns against his own government a second time.
This wasn't even the first issue in which Rogers went against the President. In Captain America #175, Captain America battled President Nixon, who (in the Marvel Universe) committed suicide in the Over Office when his plans to take over the country were foiled. Combined with the events of Avengers #63, it's no wonder that Captain America fought against his government again, and a small miracle that he didn't fight back sooner.
