It's no secret that the bad guys get the cool stuff. It's pretty much the standard in fiction for the antagonists to look really intimidating. But why is it that Hollywood always has to take that cool mask away?
Common sense gives us a really simple answer. Studios sign actors to a contract and they want to give those big names as much face time as possible. That's hard to do when they're wearing a mask. So no matter how cool the mask is, it inevitably comes off. It's a phenomenon that has only become more apparent as superhero films have become more popular.
The most noticeable instance of this has to be Venom in "Spider-Man 3." Spider-Man's iconic symbiotic antagonist makes its big-screen debut portrayed by Topher Grace of "That 70's Show" fame. Grace's Eddie Brock bonds with Venom to seek vengeance on Peter Parker; the only problem is that every time Venom speaks the villain's iconic face peels back to reveal Eric Foreman. The film does fans the favor of bringing a popular character to the silver screen, but it totally undercuts that by keeping the iconic look out of the limelight in favor of giving Grace more face time. This isn't the only time this happened with Spider-Man. In "Spider-Man", the Green Goblin regularly opens the eyes of his mask solely to remind viewers that Willem Dafoe is behind the mask. And it goes well beyond the confines of "Spider-Man" films.
"Batman Begins" features the Scarecrow, but he only wears his mask a select few times, and only very briefly in each instance. "Iron Man 2" completely does away with Whiplash's mask from the comics. The "X-Men" films keep Ian McKellen and Michael Fassbender out of Magneto's infamous helmet as much as possible. Jack Nicholson, Heath Ledger, and Jared Leto all appear without the Joker's signature white face at least once in their respective Joker portrayals. The list goes on.
This phenomenon really amounts to an example of Hollywood believing in itself before believing in the source material. A good villain often makes for a good superhero story and many of the most popular supervillains gained that popularity by looking really cool while doing what they do. Hollywood seems to have some trouble reconciling that with its need to offer big name actors as much face time as possible. It isn't a major detriment to most films, but it still seems like a final barrier in really embracing comic book tropes.
There are signs that this may be changing. "X-Men Apocalypse" kept the popular Oscar Isaac in full make-up throughout his role as the titular antagonist, and "Avengers: Age of Ultron" wasn't afraid to keep James Spader behind the camera as he voiced the entirely CGI villain, Ultron. These recent instances seem like signs that maybe Hollywood will start allowing its villains to just keep the mask on.