Yes, but Cotto is not an average boxer, he's got very good boxing skills, which is why he was able to to take so many rounds during the first half of the fight. It was Margarito's deadly pressure that broke Cotto down in the end.
Of course that's what happened, the damage Cotto took and the amount of blood lost just broke him down till he had nothing.
That's true but keeping up the superior boxing abilities is what some can't do after 12 rounds of constant pressure, Margarito's elite stamina and ability to take a punch is what makes these fighters gas out and then he starts to shine late in the fight, which is also the reason why he doesn't look too good early.