I mean, it's not like he just punches out Hulk. He punches him over and over. One punch at maximum strength is like a pebble. But if you throw pebbles, and pebbles, and pebbles, and pebbles, at someone, eventually they will get hurt. Or at least, that's the reasoning behind the Hulk and Thor fights, although the Thor fight is kind of ridiculous because Thor has slightly FTL reflexes. I mean, Spidey's hella fast, sure, but light speed? Maybe it's the Spidey Sense.
I remember the Thor fight. IIRC that's not the actual Thor, it's the guy who eventually became Thunderstrike. He had gained Thor's power and appearange but didn't know how to use his powers yet.
The pebble analogy is a good one, though even then, I think you'd have to be able to be able to punch through tank armor to even irritate the Hulk.