I dont want to feed the hate but imo, the question would rather be "Why wouldn't the creators of similar flash games be paid?"
There are people who actually made the graphics, the code, the scenario, the level design, and that game has a good couple of hours of content.
But I understand such question, I myself find The Binding of Isaac is an ugly game and, as you say, looks and plays pretty much like a flash game. If people don't want to play, they can just move on.