Why was Emile banned?
Rousseau's work sought to upset the proverbial "apple cart" of how society was seen and how it should be seen. Of the many ideas evident in Emile, the most dominant is that the existing social order is no way to educate a child. This causes a great deal of consternation when read and and received by the French public. Being the political thinker that he was, Rousseau, not surprisingly, blames much of education's failure on the social order the does not encourage critical thinking, but rather need to convey conformity to all. Rousseau's idea of "cities destroy men" and his continuing belief seen in his political thinking that individuals are "born free, but live in chains," is extrapolated in Emile to become associated with the idea that society is wrong and the more children get away from it, the better off they will be.
The reception to Emile was one where individuals saw the work as a critique of society and a condemnation of traditional means of education. They were right. Rousseau meant for the work to be transformative, calling for a complete mental and physical overhaul in how children are educated. In the end, Rousseau's work was one that caused damage and consternation to the French notion of social self, one that was pleased with where it was and convinced that what it was doing was right. This is something that Rousseau rebuked and definitely rejected through his work, causing such an intense reception to it.