If there is anything audiences could learn from Marvel's Civil War event, it's that even good men like Iron Man and Captain America are capable of stooping to lows if it means winning a war. One of the darkest lows that either man went to during this story arc came during an oft-forgotten one-shot by Frank Tieri and Staz Johnson called Civil War: War Crimes. In it, Tony Stark has the audacity to strike a deal with the devil himself in the form of Wilson Fisk.
During the latter's prison sentence, Iron Man agrees to give the Kingpin a pardon if he gives him information on where to find Captain America's team. They shake on it and the deal is done. Except, when it's Fisk's time to pay his end of the bargain in exchange for his freedom, the safehouse which Kingpin directs Iron Man and his strike force to is actually a warehouse filled with villains who the heroes are forced to fight.
There are two reasons Kingpin would throw away a chance at early release so easily. For one, it's merely payback as Kingpin calls back to a time when his warehouse was raided by Iron Man's allies. Kingpin and Iron Man are enemies after all, even if Fisk and Stark usually operate in different circles. The bigger answer though is far simpler; Captain America asked first.
Due to the often morally gray nature of Iron Man, it doesn't come off as too shocking to see him so willing to shake hands with someone like Kingpin. However, seeing the often morally righteous Captain America throw away his morals in favor of striking a deal of his own highlights the high stakes of not only Marvel's Civil War but also war in general. There's no place in a war for good people or bad people. There are only soldiers.
Since Captain America was born into a war with a soldier's mentality, that's how he was able to win this particular chess battle against Tony Stark. Hercules actually articulates it best in the comic's end. In his own words when justifying his deal with Fisk, Hercules says Cap, "doth recognize that sometimes in war, hard decisions must be made to achieve thy goal. And should that cost thee a piece of thy soul? So be it." Sacrifices must be made in wars and sometimes, it is one's moral compass that gets sacrificed. War demands scars that will never heal. Captain America paid that price against Iron Man during Marvel's prolific Civil War and he's never quite been the same since.