Shit that turned into a novel.
The hate comes from people borrowing ideas whole cloth and adding or changing little other than the graphics.
There's a term in copyright and IP, called "transformative." When a work is transformative, i.e. when what it does with the original source material alters it to the point it becomes unique, it is freed of legal restrictions. (I'm paraphrasing here.)
That usually involves borrowing from the actual source material, which doesn't happen in games. Rarely does anyone get access to the actual source code, and when they do, it's usually because the original project has become defunct. Still, the same general feeling from video game consumers exists despite the absence of concrete legal issues. Gamers can tell when something is straight cribbed from another game...usually by its lack of quality or nuance in comparison.
For me I just get genre weariness. It was at its peak for me when Towns, Gnomoria and other DF-like games were getting made, because they had a very specific look and goal yet fell way short of what they were aiming for, which was to have the scope of DF but be easier to play.
It's really bad now for less iconic games and genres. The genre of "indie 2d platformer" is so bloated now, I feel like I'm at the bookstore browsing the "Fantasy" section for how many games I see that make my eyes glaze over when I'm on the Steam store. That's less of a cloning problem and more of just a general originality problem (2d platformers seem so obsessed with visuals and tone that they've forgotten all the other shit that made platformers fun to play. They toss in a couple puzzle mechanics like altered gravity or something and call it good.)
That said I think calling stuff "clones" happens less than it used to. I basically reserve the term for when people directly mention the game that inspired them and are constantly comparing themselves to them, and their mechanics are as 1:1 with the original game as they can achieve.
For me, the hate comes from games that are asking you to get excited because you like game X, but their game Y doesn't actually do most or any of the things that made game X so exciting. Or does them half-assed. I want to get excited for a game on its own merits, not on the merits of a game I already enjoy. To make it short and sweet: I hate hype-building exercises for new games based simply on my like of a genre. Ideas get me excited; simple workman-like products do not.
Take for example Phoenix Point. At a glance you could call it an XCOM clone. But it's not. There's clearly other things at work in the game (or will be at work in game) which set it apart from its inspiration even if the format is largely the same. If it had pitched itself as "Hey I'm making a game like XCOM where you shoot monsters and manage a team! There will be research and permadeath and a memorial board!" I wouldn't have given it a second glance.
Compare and contrast DF to "my new DF-like!" which has 7 guys you can't directly order. You can designate some rocks for digging and trees for chopping and flowers for picking, combat is automated and maybe if you dig deep enough some powerful monsters appear. Units eat and sleep and grow old, and their happy bar depletes when they get hurt or don't have a bed or get rained on. Some new guys eventually show up. Maybe it's done in the Minecraft engine to boot.
Compare and contrast Terraria and Starbound. Right out of the box, Starbound had its own ideas about what to do (even if they leaned very heavily on what makes Terraria work and the final result is mixed.) They wanted a longer form of play, with story and characters, a hub, quests, all this stuff that Terraria wasn't about in spirit or in form. That's transformative, whether you like what they ultimately ended up with or not.
And then you have games like Overwatch. Compare and contrast to TF2. Blizzard's game is transformative because they bring their own brand of aesthetics and streamlining to the game and gameplay. It's not utterly different, but just enough you have to be extra salty to call it a straight clone.
Compare and contrast Binding of Isaac to Our Darker Purpose. ODP is clearly inspired by BoI but it's got its own mechanics, its own movement and combat style. It actually had multi-screen rooms long before Binding of Isaac. It has its own fucked up little tale going on. It took what made BoI work and changed it into its own thing.
Compare and contrast survival games, which are the new zombies in indie development. The Forest? I'd say it's fairly transformative (not that I can point to a single open world survival game that set the standard for the genre, except perhaps DayZ) due to the scare and story angle. Ark? Also transformative to me for all the various things it does other than "eat, sleep, kill, harvest, build shitty house."
I don't want to shit all over someone's nascent attempt at game development but...when you come to the home of a widely popular, possibly genre-defining game and announce a thing you're working on, that has no original ideas in it AND it's in a state of pre-alpha development, and you expect people's enthusiastic support for it rather than their skepticism....I can't really blame anyone for labeling it a clone and saying they're not interested. The market is flooded with games now because they're easier than ever to make and sell; gamers use the tools they can to separate games into two piles: that which excites them and that which does not. It's useful heuristic for gamers to go "i've seen this exact gameplay in another game, only done better. Why should I play your game?" Sure it blows for new developers who are excited just to have reached the point they're at, when they're months or even years away from completion, and they either want or need support for their efforts. Self-promotion is a thing now and not everyone makes a good spokesperson for their own game, nor do they know when is a good time to talk about it.
Me playing games isn't like a charity effort so a new developer can feel good about themselves though. I reserve my enthusiasm and patronage for things that genuinely interest me because the game itself is intriguing. There's just simply too fucking many games now for me to support even a fraction of what I find interesting, and it's doubly hard to be enthusiastic about *just* a "2d colony management sim with dwarves like DF" or "2d roguelike where you explore dungeons like Stone Soup" or "topdown shooter like Binding of Isaac." Those lack the crucial details that make the game different, standout, interesting, worth the risk to gamble my time and money on the experience hoping that it will be different from the games I already enjoy and fulfilling in its own special way. And there's often no real other details beyond those basics.
If the best a developer can muster is to call their game "like other another game" in its genre to get my attention, I don't feel the least bit of compunction in labeling it a clone in my head and moving on to projects that rise above the most basic bar of "what box do you fit in to." Developers don't need to ever compare their game to other games unless asked; the public is more than willing to say "I recognize this style of gameplay from game X." If your game is original enough, that's not a bad thing. If it's not, then it is seen as a bad thing.
Sometimes it seems like the real motivation is just to do game X but in their own image. Which is fine, I think every creative person has that vibe. I think if most developers were honest about that people might not play their games still but they wouldn't get as much hate or accusations of being a clone...mostly because they've honestly copped to it ahead of time.
As a last example I think Rimworld is interesting because I would absolutely count it as a clone, I've watched my roommate play enough of it at this point I can point directly to its inspirations of DF.
But RW goes beyond simply cloning DF by adding its own things. Technology. Different monsters and species. Temperature as it relates to unit happiness and survival. Different modes and starting scenarios. Other stuff. Despite looking like DF at a distance and even playing like DF in some specific examples, it is its own game. Because it's not just a cheap amateur effort to emulate its idol and maybe make some money off Steam, get a little internet famous off of people's willingness to try something that looks like something else they like. The dude has passion, good ideas, a good work ethic and he's competent. That's why despite all the similarities to DF and my inability to see it as much other than a sci-fi clone of DF with less going on than in DF at this time, it doesn't get my hate because it's doing it RIGHT. It's transformative.