The comparison is with Iron Man (with suit) and not Tony Stark (without suit). Granted that without his suit, Stark would be pretty much powerless in front of Captain America, but in suit, we have seen his prowess surpass him in many instances.
For instance, we see in Avengers (2012) that Captain America is struggling to overcome Loki in Berlin and Iron Man comes to his rescue overpowering the Loki pretty easily.
Yet, at the end of the Avengers, Captain America tries to 'take charge' and give orders to the rest of the Avengers. Is there any circumstance in the Marvel universe when both these super-heroes have to match their strength against one another?
As far as my observation goes, here are some advantages that Iron Man has over Captain America:
- Iron Man can apparently fly long distances without parachutes and Captain America cannot.
- Iron Man has special weapons under his sleeves that Captain America doesn't.
- Iron Man is built from Metal - Captain America just has serum-enhanced, but only 'human' features that may not match with metal.
OTOH, I don't see Captain America having any special powers that Iron Man doesn't. Does he have any?