Because the developers aren't the most well versed in history either.
To a degree it's a stereotype.
They know some history, they just don't know any geography
[More to the point, they were really originally using Aztec to represent pre-Colombian Central America in general, and so I think they had a lot of Maya flavor in their head.]
I can see that it might well be best for gameplay for jungle areas to be decent settlement sites. They take up too much of the map otherwise. But I just don't like that they can be *better* than grasslands.
With the science bonus, a jungle trading post or jungle farm gives more yield than a grassland does. Jungle areas are already more flexible, in that you can build in the jungle for food tiles, or chop the jungle and get production from the plains. IIRC, building plantation on banana-jungle and not chopping the jungle means you get more yield than from almost any other tile (because the -1 production penalty doesn't kick in).
And of course with the jungle pantheon beliefs, they can be insane. [Pantheon beliefs on a tile type IMO only work if that tile type is undesirable, like desert or tundra; if jungle is not undesirable, then the pantheon beliefs should be limited to bananas or similar, not functioning on every tile.]
Slightly slower improvement construction time doesn't feel like enough of a downside to compensate for higher yields.