First, every comic book hero secret identity only functions because as the audience, we decide to believe it. Even the masked heroes require a a major grain of salt to believe their secret identities would stay secret.
For instance, once the police realized that Spider-man is targeting people who all look alike, it would be a pretty quick path to Peter's door step. Any cop who had interacted with Spiderman would know that it was a teenager. But as the audience, we choose to believe it works.
So, in realty it would take no time for people who come in contact with Clark AND Superman to make the connection. However, Not that many people are gong to come in contact with both.
It is actually pretty easy to be invisible in a big city work environment and as a stringer, it really doesn't sound like Clark is planning on "hanging out" at the Planet anyway. So long as they don't turn him into the world famous journalist and author, Clark is pretty safe, so long as he keeps a distance from everyone who works at the Planet when he is Superman. How many metropolitan news paper reporters could you pick out of a line up? It is the rare print reporter who because "famous" in the real world.
I think it is set up for Perry to know and not say anything based on his telling Lois he thinks she is right to kill the story because of how the world would react if they knew a person like that existed. That translates easily to "imagine what people would do if they knew who he really was...."
I think Swanwick will definitely be in the know and act as the liaison between the government and Superman.
So, the short answer is, if the writer's put any real effort into they can keep his Daily Planet Clark identity pretty safe so long as the writers are thoughtful and creative.
Let's face it: Superman's secret identity is inherently ridiculous. There's no getting around it. If Snyder and Goyer were to augment his disguise in any way by giving him a fake beard or something, there would be a huge fan outcry for not staying true to the original character.
We all want the traditional bespectacled and clean-shaven Clark, yet at the same time we want to believe the secret identity is realistic. Sorry guys, but there's just no way to square that circle. It all comes down to three simple words: suspension of disbelief.
That said, I think that last post by kalelvis brilliantly summarized some of the inherent problems with the "secret identity" trope and some of the creative ways that the writers of MOS 2 could get around them.
Take any real world person Superman would be as famous as:
Elvis Presley
Michael Jordan
The President of the United States
Madonna
Do you ever think the above people have other or "secret" identities?
Do you suspect that you maybe secretly work with Madonna? Michael Jordan? Obama?
No. Why not?
Because, like Superman, these celebs don't wear masks. You assume that Michael Jordan is living as Michael Jordan all of the time.
People aren't necessarily looking for Superman's secret identity...they don't know he has one. Also, Kal El is the name that the public is aware of.
The fact that Superman is not disguised diffuses MUCH of the mystery that comes along with Batman, Spider-Man, and The Lone Ranger.
Problem solved.

Because all those celebrities have people around them all the time. And they don't have super-powers, so I don't think they can fly away faster than they can be tracked.
On the contrary, Superman is not a celebrity. For the world, he is an alien and they have just seen what that race can do to the world. I'd say that many people must be worried that there's an alien potentially able to destroy the world among us.
I don't get your point about Spider-man. NYP is probably looking for a lot of different criminals, why would they think that Spider-man has a specific man in mind? Specially after he confronts the Lizard?
That said, we don't just decide to believe that Clark can hide his identity with glasses. Writers and movie makers do things to make us easier to believe. In Reeve's case, they had more than just the glasses. In this case, Lois Lane and a lot of different people know. I don't think the tone of MOS is enough to throw a pair of glasses and nothing else in this regard.
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yup, they can shortlist. Clark Kent should be in the data base.with facial recognition in the modern age the military would know who he is within days
Is it farfetched if they used the sci-fi elements of the mythos to get around the ridiculousness of the disguise? Like, imbuing the glasses with a mild mind-fogging properties that can also affect electronic devices that could capture and record pictures?
Still, in this movie, I got the sense that he had some psychic ability. Remember that scene where he was hiding in the closet? It seemed like he was hearing the thoughts of the other kids.
are you refering the school bus scene?I thought he looked surprisingly different when he showed up at the DP, less intimidating and masculine. But one problem I did have with this movie was everyone and their mother knowing Clark was superman/an alien. I don't want some Blur bull crap but dang could be try to hide his face a little!
He can always just rotate the earth a few times to wipe the slate clean. Everyone seems to love when he did that lame a$$ move so why not do it here.
Yeah, I've met a few famous people, and didn't recognize them immediately. It's kind of funny how unremarkable some of them were in person. Then again, at the end of the day they're just humans (probably).
But again, it does sort of bastardize Clark Kent. I mean, he might as well have become a janitor in a police station. I much prefer him actually wanting to be a journalist, as opposed to it just being a cover story for his activities as Superman.
They've played around with that, and I always found it too farfetched.
In some stories, Superman had the ability to hypnotize. In others his eyes have some weird effect. In some stories as I recall he even compressed his spine to appear shorter as Clark Kent.
Still, in this movie, I got the sense that he had some psychic ability. Remember that scene where he was hiding in the closet? It seemed like he was hearing the thoughts of the other kids.
It's funny, ever since the Rotten Tomatoes average dropped below 60%, there are lots of spiteful references to the Donner movies in discussions about Man of Steel.