Here's my personal theory about the Elantrians:
Before Elantris (the city complex) existed, things were different. Some people were connected to the Dor via the land, and some weren't, just like we see in the story. The ones who were connected were not very different, however. Perhaps they were a little bit stronger, a little bit more healthy, but it's not like they would glow in the dark. The main difference, however, was that they could draw Aons. Weak Aons, like what Raoden could do before fixing the Dor, but they still would have enough power to make a difference. It would also be enough power to create an alphabet and discover some of the theory.
The next bit is more speculative. It seems likely that the people who could draw Aons (ur-Elantrians?) would deliberately keep secrets and try to maintain an aura of mysticism about their capabilities. They would also try to understand their powers more carefully. Thus they probably formed societies for the express purpose of studying what they could do in a systematic way. I think we can assume that at some point, one of these groups realized that if they created a large enough Aon, they could boost their abilities enormously. So they did it. But to maintain authority, they deliberately obfuscated why they did it from the common folk. It was their ace in the hole, and they didn't realize it could be destroyed so easily.
As to why nobody tried to fix Elantris: That's actually explained in-story. The shock of loosing the Dor was apparently very large, and those Elantrians who experienced it were in no position to explain anything to anybody. Combine that with the deliberate coup lead by the merchants, and years of pent-up resentment against Elantris, and you have the perfect combination for almost willful ignorance. The rebellion was a stupid idea, but people have done stunningly stupid things in the history of our world. (The Soviet Union and artificial famines, anybody?)
One other thing: It is made perfectly clear in the book that only Elantrians could have drawn the line the finish the Aon. With all the old Elantrians reeling in shock and the new ones confused and in a world of hurt, there was nobody who knew what to do who could also do it.