I used to have a (high-ranking and well-educated) foreign colleague who used to think that the "Main" indeed signified that this was the bigger and more significant of multiple Frankfurts.
I honestly can't blame him, it was a deceptivley plausible misconception.
The German city name Frankfurt isn't unique. That's why the cities often have an identifier. The biggest and most well known Frankfurt is located at the river Main and therefore called Frankfurt (Main). Main is also used as description in programming which is where the rest of the joke is coming from.