This song takes the video to a whole new level of incredibly bad. The way it cuts off at the end makes it worse because now you don't have bad song closure.
My research indicates that it's got to with the crossover appeal between Sonic and Rainbow Dash. They are both blue, they both have attitudes, and they are both super fast. SoniDash is a popular 'ship, so that gets Sonic fans thinking about ponies and pony fans thinking about Sonic. Also, I'd imagine that there's a lot of overlap between bronies and the sorts of people who enjoy the Sonic Expanded Universe.
You've also got to remember that ponies have become one of the most successful memes of our time, and people have been making pony crossovers with pretty much everything. For example:
Mario Ponies - http://fav.me/d5cmxg5
Gravity Falls Ponies - http://fav.me/d5ehwf8
Adventure Time Ponies - http://fav.me/d63fm8f
Dostoyevsky Ponies - http://fav.me/d607c6b
Hitler Ponies - http://fav.me/d500sw9