"I run errands when I'm told to." There's no spite in his tone - just the same relaxed balance of professional and amicable. "But yeah, I know how to fly. I'd be flying now, but for some reason they insisted the cargo shouldn't be left unattended."

And by cargo, he mostly means Bruce Banner. S.H.I.E.L.D. isn't particularly concerned about Howard Stark doing damage, at least not while he's so far from a lab.