Maria Respects Captain America as much as she sadly mistrusts him.
The problem, as she sees it, is a difference in timezones; He was born back when the bad guys were easy to tell and war was more straightforward. The intervening decades had not seen humanity change for the better, and he knew it.
So he has an insubordinate streak, because he will always do what is right over what he is ordered, especially if he doesn't see the reasons behind the order. He was a brilliant tactician himself, but he thought in more straight lines, because he was honest.
SHIELD thought in twisty corkscrews, and sometimes did the wrong thing for the right reasons, and their secrets had secrets.
Cap knew secrets eventually came back to bite the keeper in the ass.
This would eventually be a problem, and Maria Hill just knew it.