There's a lot that ultimately goes into this -- on the primary thread subject, that is. (I would diagram this to make it easier to follow but this ain't wiki, so we're probably all fucked if my usual communication fail is in play. Sorry, y'all. Seriously, this is some flowchart-requiring shit.)
First: is it reality, or perception?
Frankly, much as we may not want to admit it, sometimes it is the reality. If it's the reality, why?
People can be cliquish in the bad way; sometimes they realize it and sometimes they don't. People can be exclusionary or distrustful or might simply be jerks. They might just be there to hang out with a handful of close friends that are the only thing keeping them in the hobby at all these days and not have time in their RL schedule for more, which, while it isn't deliberately exclusionary or any value judgment on the outside party, ultimately has the same end result.
More complicated is this: sometimes it isn't the other people. Sometimes it's us. Sometimes what we want out of the game is not what the game is designed to be, or is out of step with the game's culture. Sometimes games will adapt or players will play along or find these new avenues interesting, but that's a case of fighting inertia, which realistically is not often going to be a very successful prospect. It doesn't mean we're doing something wrong, or that what we want is somehow bad or wrong, it's just not what the game culture has evolved to be or include. The people who go there generally go there because they like what it is and what it currently offers. (Though plenty of us play on games despite what they are, and everyone sucks something up to a greater or lesser degree about any given game, the good has to outweigh the bad for anybody remotely sane to stick around.)
'Fish out of water' can be a fun character type to play, but it happens on the player level, too. Sometimes people shy away from players like this because they just don't get what that player is trying to do, or feel they're out of sync with what drew them to the game in the first place. Again, what I'm talking about isn't something bad about the game itself or about the player who feels excluded, but of the player having different expectations of the game and/or its culture in a way that hasn't been addressed directly in the thread before (as it was with the 'level of welcome/invitation to things'). Examples:
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A highly PvP-focused player arrives on a game with a long-standing exclusively PvE culture and proceeds to play as they always have elsewhere.
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A player accustomed to highly specific code for many details of their existence, such as an RPI might have, arrives on a game with minimal code, and asks where the commands to make sure they've eaten that day are, then requests staff add these things because 'it's just not a game without them'.
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A player seeking an elaborate and in-depth metaplot and major staff storyteller presence guiding the course of events arrives on a sandbox game, where staff primarily alter the world to reflect what they players have impacted the setting if the players run plots and events that create these changes on their own initiative.
...none of these wants, play styles, etc. are bad or wrong. They're simply a better or worse fit for any given game. No game is going to be all things to all people, and it's a mistake to try. (It's a recipe for failure.)
These things can contribute to making a player unwelcome in reality in two important ways: other players may feel they're unwelcome or not want to interact with them, or, more subtly -- but I think a lot more commonly -- the player feels they don't fit.
I think there's a lot more self-awareness on this latter front than there once was; I know I see a lot more 'the place is fine, it's just not for me/it's not my style/it wasn't what I'm looking for' than I did years back. The sad truth is, not everybody has that self-awareness. They just see people shying away, and may not understand why, or how their expectations are impacting the situation. Without that awareness, they're just left with the sting, uncertainty, and feeling more and more unwelcome. (Which sucks.)
Even the generally more with-it folks I know, I've often seen say things like, "That game is just dumb because <reason that boils down to it not being exactly the opposite of everything it says it actually is>!" No, the game isn't stupid. You just want something out of it that it isn't designed or intended to provide for you. (Another reason that labeling intent and focus is important.) It doesn't make you stupid, either, but it's still something of a self-awareness fail. I do not go to Taco Bell and order Chinese food, after all -- so why would I go to a game labeled 'sandbox' and expect to be fed endless metaplot and staff-led PrPs? Why would I go to a game with heavy code and expect to just be able to ignore it all because I personally find it no fun to interact with extensive code?
All of that can contribute to a wholly internal sense of 'what I want isn't what I'm getting here', which, unless somebody's really paying attention to the fine points, can feel a hell of a lot like 'I'm not wanted here' after a while. It's understandable from both sides: you're looking for something the game doesn't really provide, and you're asking for something the game's culture has not evolved to give you. While there are rare exceptions, generally, this is going to lead to someone being progressively less involved with others on the game. You're not getting what it is you're really looking for, so you invest less. You're asking people for something that isn't what they're interested in, so they take you up on your offers less or invite you around less.
Both of these reactions are entirely normal and they are not indicative of 'bad' or 'wrong' or anything of the kind. They're pretty much the standard evolution of this rather typical reality. That process of weighing the good and the bad of a place to determine whether you're going to stay or not? As this progresses, 'leave' tends to get more appealing, even if the player trying to balance those scales isn't entirely aware of why.
It's a lot more subtle than being outright ignored in a scene, or having no one respond to offers of RP, but I have a strong suspicion it is a lot more common than either of those things are or ever will be.
...as to the perception thing, that's kinda been covered already.
