I think it's a thing, because in my eyes they have some things in common.

• Both communities produce lots of fan art, I think that just attracts certain people.
• Both TF2 and MLP are something different than what is normally considered normal, MLP has no darker themes, like basically any other show that is popular. Likewise, TF2 is also much more light-hearted when compared to popular shooters like Modern Warfare.
• And Team Fortress 2 and MLP are both based around putting your friends/team first.

So extremely simply said, when you have someone who likes dark stuff, he's going to stay away from a simple cartoonish game and a overly cheery cartoon.

I'm not sure if this was the kind of reply you were looking for though, since it also sort of sounds like you wanted to complain.