So apparently the things you did and said two years ago define who you are today? That's the most retarded childish thing I have ever heard of.
Let me try to explain why they're hated.
The four top teams in the world are Virtus Pro, Envyus, Nip and Fnatic, but out of those four VP, NV and NiP are the only ones with a dedicated, large, vocal, arguably young (NiP and NV more-so than VP) fanbases.
Virtus Pro has gained their following by being very charismatic, they are very easy to look up to, Envyus through pandering and fan interaction, and NiP just through history of being the best team in the world for a really long period of time.
The Fnatic guys are some of the best players in the world, but they are not outspoken. They don't present themselves all that much in social media. They don't stream and such. They just play the game. They aren't really big on fan interaction. They don't have that long history of being the best in the world or anything. That's why they don't really have a large dedicated fanbase (yet?).
Lets make one thing clear: fanboys are cancer. The only thing fanboys care about is their own team. They don't care about the scene itself, just the team. They will go out of their way to make their team look the best, even if it was required to bring down a rivaling team.
While the pro's are battling it out in the game, the fanboys are having an all out war outside the game. Fnatic doesn't have as large of a dedicated fanbase as the rest of the team, so they're an easy target, it's easy to attack the team with accusations since there's no one really there to "protect" them.
It seems like it baffles people that a team like Fnatic could be so good. Like, "who are these guys even I've never heard of them". They can't accept it. "What the fuck is a Flusha? Whatever it is there's no way he is that good he must be cheating".
The hate that Fnatic has gathered is the result of fanboys trying to defend their favorite team by accusing of fnatic with shit (instead of actually talking about their favorite team).
It's almost like Fnatic is the uniting factor for all fanboys. An unpopular team being the best in the world. "Oh you hate fnatic too, you're cool then I guess". Which kinda means that there's this Fnatic vs The World situation going on in the scene.
TLDR: Fnatic vs The World mentality. Not really presenting them in social media or trying to make fans. No large established fanbase to fight back the hate.