It's curious that the other Brony sites are unaffected, so far. Will the axe fall on those as well. I wonder if this has anything to do with them hiring a new exec of marketing who has a different idea of fan-art, screen captures, and posting videos of the show.

I'm not sure, but that "friendship"- the willingness to allow the videos to be posted- helped keep the Brony fanbase going. You'd think a fanbase of People who actually make money to spend would be more welcomed.
If the other sites DO go down (this is actually the second one I've heard this happen to) then theyre going to end up losing half their fan base (there's a friggen Bronycon for cryin out loud, do they not realize this?)

Exactly my idea. Not only will they loose the fanbase but they'll build active hatred as well. I've noticed many links to MLP: FiM videos on YouTube are also not working, the videos are getting removed from YouTube.

granted, but there's a con for pretty much everything nowadays... having a convention isn't a very accurate litmus as to something's actual popularity.

besides, if they were hosting videos to watch, they're obligated to send C&D letters or they risk losing the rights to their copyrights.

Maybe, but it went beyond just having a convention. Things like the show getting extended beyond the first season, the price that fan made plush dolls have been going for on Ebay despite the horrible economy, and the sheer amount of fan made creations based on this show give more power to the notion it's a popular show.