Here's the full quote:
"He wants to serve his country, but he's not this sort of jingoistic American flag-waver," Johnston said. "He's just a good person. We make a point of that in the script: Don't change who you are once you go from Steve Rogers to this super-soldier; you have to stay who you are inside, that's really what's important more than your strength and everything. It'll be interesting and fun to put a different spin on the character and one that the fans are really going to appreciate."
Now, if we want to pick apart the language being used, pay close attention to the phrase "jingoistic American flag-waver."
Let's also consider where Johnston is coming from. Here's a guy who probably grew up in the midst of the disillusionment that much of his generation felt in the wake of Vietnam. For them, Captain America was this ironic icon of all that was wrong with the country: blind patriotism, follow-your-orders-without-question, staid, rigidly moral 1950s crap that no longer existed to them. It's understandable that he wouldn't be making a 1940s serial.
Let's also keep in mind that Cap has to transition between the 1940s and modern day. And while he may have some anachronistic holdover behavior that'll make for humorous moments, and maybe some real serious earnest ideals that don't fit in a cynical modern environment (that being the point), that's most certainly NOT the same thing as some dumb-as-rocks boyscout who just blindly follows his mission.
I would hope that what Johnston is trying to say is that Steve Rogers -- as Cap -- went into the war as a man of conscience who wanted to embody the best of what America has to offer, but who doesn't necessarily act obnoxiously about it. He's not Team America: World Police. He's something more grounded and less over the top than that.
I think it'd be VERY easy for a bad director to turn Cap into a parody of himself, as some stupid "AMERICA!!!! **** YEAH!!" kind of guy. It wouldn't be hard to do.
And let's not forget either that Cap in the 70s and 80s was someone who believed in the overall mission and in his country more than just in what his politician bosses tell him to do. Anyone remember when he went as The Captain? Or how about the recent Civil War stuff where he fought against registration? Basically, Cap isn't blindly jingoistic (as in, loves war), nor a reflexively law-and-order-the-bosses-told-me-to-do-it type.
He's someone who loves his country and what he believes it represents, and he's proud to be a symbol in that cause. I guess, to me, I make a distinction between someone who's a "jingoistic American flag waver" and someone who genuinely loves the ideals this country stands for. Those two things aren't at all the same. So, yeah, I agree with Johnston that that's NOT what Cap is.
Now, as for the "different spin", I have no idea what he's talking about, unless he means "different" from "jingoistic American flag-waver." In which case, I'd assume that means "different from what a lot of people reflexively think Cap is, just because he wears the stars and stripes."
Check out Frank Miller's run on Daredevil in the Born Again TPB. Cap makes an appearance in there and, to me, it sort of embodies who Cap is. He'll break the law and disobey orders when those orders are, in his view, illegal. He deeply loves this country, including the symbolism (yes, the flag), and recognizes what it means, but he also doesn't blindly kowtow to authorities. I think you can make a film with all of that set in WWII, keeping the character very idealistic, as long as those ideals don't simply boil down to Team America.