You may remember The Road To El Dorado as one of the few bombs in the otherwise uber-successful Dreamworks lineup. It came out back in 2000 and was loosely based on legend, which I'll explain in this piece.
While it may be true that some scholars thought the famous land you probably learned about in high school, Tenochtitlan (below), was El Dorado, It was actually a fictional "legendary" place that many Native Americans used to distract the Conquistadors (love that word, by the way) to lead them farther away from their own villages.
If you recall, the evil sorceror leads Cortes to the old destroyed entrance and Cortes, upset and distraught, believes the sorceror has lied and enslaves him.
In reality, it wasn't uncommon for one villager to "take one for the team" so to speak, leading Conquistadors to the fictional land to get them as far away as possible from their home village. That person knew that they were probably going to die, but they were saving many lives by leading these travelers astray - and likely pissing them off in the process.
There were also stories of "bird men" and a tribe with ears that hang down to their feet. The Spanish believed these stories as well. You have to think about the fact that nobody at this time could really verify much. I mean, this was the "New World" and it was uncharted territory.
The movie was a little dicey and was met with some criticism from Mexican-Americans who believed the depiction of their ancestors incorrectly showed them as immoral and barbaric. This, of course, is juxtaposed to the fact that many of these Natives were victims of intense genocide and the murder of 95% of their population at the hand of Spanish Conquistadors.
Whenever you deal with a touchy subject like this in an animated film designed for kids, real feelings can surface. I think there's a reason that this wasn't a very big hit. Fictionalizing something so complex and painful from the past isn't typically a good idea.