When I was much younger, my actual "definition" of a "novel" was a book that ended unhappily. Old Yeller, The Red Pony, Where The Red Fern Grows...decades ago that was what was in the libraries, so I read them. All the examples that people are giving of "successes" are from books written many decades ago. They probably wouldn't have much of a market now, if they were newly written.
If the bad guys win, where's the payoff for the readers? Normally, the payoff comes when a character who you, the reader, have invested in, triumphs over the antagonist. You are able to experience this victory vicariously. That's why writers deliberately create situations which readers can identify with, giving protagonists problems and characteristics that they think their readers might also have.
There are other possible payoffs, of course. Readers might not care about the characters as much as they care about the amazing worldbuilding, or the mystery, or the brilliant technology. But even those things aren't going to be enough if your reader is left feeling unsatisfied or blindsided.
If you are going to take the readers for a ride, you don't deliberately crash the car at the end of it.
Are there people who get a kick out of being in a vicarious car crash? Sure. But the target market is small, and editors aren't likely to waste publishing resources on a book with a very narrow appeal. They can only publish a limited number of books per year, and they want the greatest number of sales possible.
One exception may be the niche market of role playing novels (ie, novels whose settings are from computer and role playing games. Many of these tend to be "dark", and their readers have a much greater tolerance for Bad Stuff. I once was asked to edit a book which a friend of mine had been commissioned to write for the role playing game which he had authored. I made a lot of edits, including some plot changes. He later told me that he thought the book was a lot better after my changes, but that the editor had rejected many of them because they weren't "dark" enough. The game was set in a world of perpetual tragedy and loss and the idea that you can never really win because the opposition was just too powerful.
You might think about doing some research into that niche market, figuring out which of them your novels might be adapted into, then write a couple of chapters and pitch to them.
If you are content to self-publish or are just writing for your own pleasure, then go for it. You will probably be able to find many people who will enjoy reading what you have written and it would be a good exercise. My one guilty pleasure as a writer is fanfic. I love writing fanfic, mostly because my favorite part of a story is the conflict, and the fanfic community is all about conflict. There's a huge target audience, and for the most part the fanfic audience is quite appreciative of writers' efforts. It's a great playground to indulge in. But there's no money in it.
If you are serious about getting published by a legitimate organization, it might be better to give yourself every advantage and not try to swim against the current this early in your career. If you had already written your novel, my advice would be to go ahead and give it a shot, see if you can get any editors interested. If your story is well written enough they might take a chance.
But because it sounds like you haven't got much past the idea stage, my recommendation would be to put it on your "to be reconsidered later" and write something that has more general appeal. Writing a novel requires a serious investment of your time. Writing five of them, even more serious. And apart from the writing, there's the time you spend pitching and schmoozing and getting yourself familiar with and known by the movers and shakers in the publishing industry.
Saying "write what you love" is good advice, in the same way that you are told "follow your passion" by career guidance professors in college. If you can tolerate the poverty, sure, go ahead and get a degree in Medieval Literature. But you need to decide if you are writing "for love or for money". It's not black and white, obviously, people don't often write what they hate just because it sells, and people who write what they love even though it's unpopular sometimes can "break through" but when you are a brand new writer, you will want to give yourself every advantage.
It isn't clear from your explanation which of your character(s) are/is POV characters. A protagonist is the main character. The story is about him or her. Since your villain appears only at the beginning and the end, he is obviously not the protagonist. Normally, the POV character(s) and the protagonist are the same, but they don't have to be (the Sherlock Holmes stories are a well known example of this).
I can think of two way in which you might create a story where your bad guy wins and your readers are still satisfied by the ending.
The first is if you make your villain the main character but never enter his POV. Set readers up to admire the villain, even while the POVs hate him. When the villain wins, he does so with style, by cleverness. When the heroes win, they do it in such a way that the readers are left feeling that they didn't deserve the win. Maybe they behaved dishonorably. Or maybe they just have so much power that they overwhelmed the opposition. Sabotage them even as you hand them their victories and at the end, readers will feel that the villain deserved his win.
Another thing you might consider; make one or more of the villains into protagonists. If you don't want readers to be in your main bad guy's head, tell the story from the point of view of one of his henchmen or allies. You might want multiple points of view, from both camps. That way the readers can "root" for both, knowing that one is going to lose. You haven't said why you want the villain to win. Is it because you like him better than you like the heroes? If so, you may be choosing the wrong protagonists. Rethink your story from the villains' point of view and settle your readers in the "bad camp" and although the ending doesn't change, your readers' perception of it will.
Addition after reading comments:
The idea of having the bad guy slowly take over one of the POVs is an intriguing one, and worth pursuing. My recommendation would be that you start readers off with a very strong sense of who the antagonist is and how the POV character is very different. Maybe that difference is enough to throw the bad guy out of the good guy's head. ("No! I will not do THAT!"). Over time, remind us of who the bad guy is through what he does, and who the POV is by how he reacts to what the bad guy does. Show us the changes that are effected in the good guy because of his exposure to the bad guy. Show us how the differences between them are getting less and less.
Maybe they are both changing. Maybe at the end they can both "win". You might get rid of the characteristics in each that readers will find offensive. Maybe the good guy is kind of a wimp. Or he's arrogant. Or impulsive to a fault. Or devoted to a cause that doesn't deserve his devotion. Maybe the bad guy learns to care about something other than himself.
Or, in the end, maybe the better man wins because he's better, not because of chance or because he's stronger.
All the end of the series, there should be a feeling of inevitability that creeps up. Readers should feel that the ending was the only right choice, given the factors. They should be able to feel that they "saw it coming". Readers like to be surprised, but they do not like to be deceived. If they are expecting the hero to throw off the villain's influence once and for all, they will not be happy to learn otherwise.
When I am reading a story, I pay a lot of attention to how I feel about the characters. I expect to like the characters who are going to "win". If I don't like a person, I expect him to be defeated. All you have to do is lead your readers to like/admire the villain more than they do the "good guy" and the villain's eventual triumph will be well received.
Another way to accomplish the goal is to redefine the win. If the Dr. Strange movie had left him trapped with his nemesis for all eternity, how satisfying would that have been? (Unless they had established beforehand that there was no other way, that if Stephen escaped so would the bad guy). If your hero poisons himself just before giving in and allowing the bad guy to take him over, he wins.