Yes what? Yes, they know, yes they would assume he’s a mutant, or yes you agree ?
I forgot about Daredevil. I don’t think it would fit in, as the other movies were, you know, decent!
I intentionally left off Blade and Ghost Rider, as they are not pure superhero films. (I’ve never seen GR or B3).
Are we missing any other Marvel films (post X-Men 1)? I was including Wolverine in the X Umbrella- FYI.
You asked “wouldn’t they just assume he’s a mutant?” and I responded “yes.” 
The 2004 Punisher film? or was that a different studio?
Not if you can fly.
One of my favorite comic books was “Marvel Team-Up” which usually consisted of Spidey teaming up with other Marvel heroes.
Not sure the studio, but duly noted. There was also a sequel in the last few years.
I’d probably lump that into the Blade/Ghost Rider non-heroic, “other” category.
Spidey was close friends with Johnny Storm, who helped him build the Spider-Buggy- a dune buggy with a Spidey motif, web shooters on the headlights and a spider spotlight. Spidey eventually accidentally drove it into the harbor.
RE The Public Opinion Of Mutants
In House Of M, the world got seriously changed and many heroes ended up getting their heart’s desire. The biggest change was that mutants were loved and celebrated. This led to Spidey living in fear that people would discover that he wasn’t really a mutant.
In general, the whole ‘love the heroes and hate the mutants’ thing makes sense to me. A super soldier serum or a flying suit of techno armor is one thing. To be told that you’re a neanderthal, due to be replaced, and that your own kids or grandkids may be human only in the broadest sense of the word is quite another.
What I’d like to know, does using a character in one movie restrict it’s use in another movie?
For example, could The Punisher show up as the antagonist in a Spiderman movie?
No. However…
Also no.
Not because the Punisher appeared in his own movies, but because the film rights to the two characters are held by two different companies.
When they both revert to Marvel studios, then Punisher could appear in a Spider-Man movie, if they wanted.
IF they wanted.
That’s another however, however…
Warner Brothers/DC has been known to segregate their properties, if two franchises are going at once - Batman characters (other than Batman himself) were kept out of JLU, because The Batman was going at the same time. Wonder Woman characters apparently have the same thing going on now (though I don’t know exactly what they’re planning with Wondie that they’re keeping her cast out of things). They’re not likely to ever crossover the Batman series of movies with anyone else, because that would screw up the Nolanverse’s conceit.
Marvel may do the same thing with the non-Avengers-related properties, even after reclaiming them.
There was also an ‘Elektra’ spin off movie from Daredevil that was absolutely dreadful. I like Daredevil and Elektra in the comics, and I confess to harboring a slight crush on Jennifer Garner personally, but this was just a painfully bad movie. It’s no wonder it hasn’t been mentioned yet. 
DD was a mediocre film with some genuinely inspired moments though, such as Murdock returning home at the beginning or when he saw Elektra’s face in the rain. I absolutely loved that scene.
Re: Mutants vs. Superheroes…
I have no inherent problems with the idea of general hatred for mutants within the X-Men’s own little sphere… It only becomes a problem when contrasted against the Marvel universe as a whole. I’ve never really been able to accept the idea that the general population would necessarily be able to distinguish between altered humans and genuine mutants. The only thing that separates Cap, Spidey, or the FF from the X-Men is good publicity. Why don’t people suspect they’re all just lying?
OK, so Sue Storm’s little brother volunteered for the Super Soldier program…wait, we can make this work…ummm…
For what it’s worth, most “normal” looking mutants can fly under the radar as well. It’s only assumed you’re a mutant if you look different or if you have weird powers and don’t act like a superhero.
It’s normal for there to be Super soldiers, Norse Gods, Rich billionaires, and wacky scientists out there creating devices to save the world. That’s the norm.
The problem is when you see the freak in the corner or you see someone who stands up and proudly proclaims he’s a mutant or they see them helping other mutants. That’s when things get ugly because those people are now “different” and to be feared for their strange ways.
Close but no cigar. The Transformers were introduced in their own comic, and Spiderman appeared in issue #3 (when it was intended to be a four-issue miniseries only, so they figured they could get away with having them be in the 606 universe). When it turned out that Transformers was going to be an ongoing and not a mini (just in time for a hasty change to the ending of #4), Transformers got moved to its own universe outside the 606. And Spiderman was never spoken of again (though Circuit Breaker, a minor character in Transformers, did show up in Secret Wars II).
Anyways, to answer the OP, I’d say that X-Men are definitely their own universe. I could see Spiderman and FF being part of it, but given the different studios, they officially won’t be, so I can go with only what’s “official”.
Bonus points for El Aguila, a costumed superhero who led folks to believe from the start that some kind of blaster-ray was built into his gimmicked sword; truth is, (a) it’s a completely ordinary sword, because (b) his mutant power involves zapping folks equally well regardless of what conductive piece of metal is at hand – and he’s a terrific fencer who likes to keep his advantages quiet.
“Look, boss, against all odds I got the sword away from him, and even pinned him against the hood of a car – and the next thing I knew he was long gone and I was on the ground, waking up with a splitting headache.”
Actually, Chris Evans will be the second actor to play two different Marvel characters (Third if you count Nic Cage, but Big Daddy isn’t Marvel Universe, so…). The first, of course, is Rebecca Romijn (Mystique and Joan the Mouse).
I’m not proud of my comics geekiness, but I acknowledge it freely.
Lion’s Gate would have to let their license lapse. They made two films of the character, Punisher (which grossed $33 million domestically and had a budget of $13 million) and Punisher War Zone (which cost about $35 million and grossed around $8 million domestically). They’re a small studio and could see potential in a franchise that made them money once, even though the sequel lost them a bit more than the first one netted, but I would not be surprised if they let the license revert to Marvel next year. So yeah, he could show up as a Spider-Man antagonist at some point. If that happened, Marvel would license the character to Sony, and probably under very different terms than Spider-Man is licensed to them.
This kind of movie makes money hand over fist in foreign markets and DVD sales are worth considering. Punisher could go either way.