I haven't seen much My Little Pony as a community personally. Only FiM related things being crossed into other fandoms. "Brony" culture is an entirely different subject and unrelated to the otherwise good show. I also don't see the logic of bringing up "Mostly because of parts of the fanbase that are horrible," while simultaneously and obstinately making it known you relish in the Team Fortress community, which has it's own sizable chunk of awful fanbase. Every fandom has elitists, pricks, trolls, rookies, and dead parrots who try way too hard to be a part of the community, and if that is what you mean by "Parts of the fanbase that are exceptionally horrible," then I'm sorry to say that you will never find a fanbase of any media that will satisfy you.
That being said, again My Little Pony: Friendship is Magic is a legitimately good show, and Team Fortress a better-than-most FPS, and I have nothing but respect for you as a person. It's the intolerance and willful ignorance I don't like.
I made my statements in recognition and knowledge of "elitists, pricks, trolls, rookies, and dead parrots" in the Team Fortress 2 fanbase; indeed, they are part of every fanbase, like you said, and are simply part of human society in general.
But these are not what I consider to be "exceptionally horrible".
It is those parts of a fanbase that focus on producing exceptionally vulgar / explicit material and those with biased, overrated opinions about a work.
As for the first part, I (thankfully) don't know of any excessively vulgar fan material for Team Fortress 2. There are some instances of vulgarity, but the ones I've seen are minor and certainly not the focus of the material in question, outside of some silly YTP-style songs and word-splicing. About "intolerance", entertainment focused on unreasonable content is what I do not tolerate.
Now I may have been extremely lucky about the second part, but I have always seen mixed opinions about Team Fortress 2. Some of the most dedicated players and fans will always have a long list of faults to point out in Team Fortress 2, and rightfully so. (e.g. "This game crashes too much", "This update is broken", "This new item is unbalanced", "The game runs so slow")
I have never found in my own or other people's observations of the fanbase any opinion that regards Team Fortress 2 as perfect and faultless.
Such a perception would be hopelessly misguided, as Team Fortress 2 is far from perfect.
About the MLP:FiM fanbase, I don't know much, aside from that there are bronies that do actually "love and tolerate", and those that don't. I'm not into the show, though.
If there is any ignorance I have, it is certainly not willfull.