Most coming to mind are due to rewatching once I got away from my trad Catholic upbringing and realized Gay People Exist.
The Matrix - ok on first watch, better with the trans metaphor
Fight Club - I still don't like it, but it's def better when seeing Tyler Durden is gay
Jennifer's Body - I wasin the "I thought this was something else going in" camp based on how it was advertised. I like it way more now years later, and I like Meghan Fox more too.
The Deer Hunter. I first saw it when I was in my early teens and didn't care about the guys, the wedding, hunting, or any of the opening activities. I was not looking at the characters nor how they were reacting nor noticing themes.
I watched it again in my 40s and thought it was really good. The way the men communicate (and don't), the things that failed to stay the same for the characters, the loss, and everything -- it all felt deeply poignant. I still thought the movie was a bit too slow, but I finally 'got' why people respected it.
I had a similar experience with Lawernce of Arabia, but I liked that one as a youth and on re-watch was amazed at everything that went over my head, which made the adult viewing much better and cemented it in my mind as one of the best movies of all time. Another of the best is The Man Who Would Be King, but I've always abjectly adored that one.
I've come back to mention a few others that hit different re-watching as an adult: Zulu, Khartoum, Kim, Gunga Din, and basically any other grand epic where the Brits are portrayed as gallant heroes battling uncivilzied local populations -- until you look at it in terms of colonialism and see the Brits as pompous captialists parroting government lines about their own greatness and glossing over the legitimate reasons the locals want the colonizers gone.
Unrelated: everyone watches the movie Falling Down as if the lead is our Hero, but try watching it (as I did) seeing him as the unhinged villian.
I mean, I guess there will always be people who comically miss the point of a given piece of media (e.g. the lionization of Al Pacino's Scarface, or "Born in the USA" playing at political rallies), but you make it sound like you've unlocked some secret meaning in the film by viewing Michael Douglas as a villain. However, that's not even the subtext of the movie, it's the text itself. Douglas says, practically to the camera (if I'm remembering correctly, it's been several years), "I'm the bad guy? When did that happen?".
Anyone who walked out of the movie thinking it was sympathetic to its protagonist wasn't paying attention. Again, I know these people exist, I'm just flummoxed by that fact.
Okay, I shouldn't have said 'everyone', but people in the theater cheered for him -- and when the movie let out, I heard people putting him in the hero role. I'm glad to hear a wider audience saw it as I did.
Hot Fuzz. I thought the film was stupid. Then one day it was on TV again and it just clicked. I accepted the stupid and enjoyed the film for what it was.