Can you play as the Native Americans?

I don't know about any such mod and even if it would exist, chances are low that it would be fun to play, as in the code most game features are just disabled for the Natives.
 
Colonization 2071 allows you to play natives, though they renamed them to aliens. As already mentioned, a whole lot of features are disabled for natives, which are enabled in col2071 or playing aliens would really suck.

I don't think that is what you had in mind, but I think that is what is currently possible. I once tried playing natives in RaR (I had to modify XML to do so) and I didn't even manage to finish the first turn without the game crashing. It's simply not designed to handle human inputs to natives.
 
There have been several posts from people interested in playable Natives over the years, with a fuller discussion of what's involved in making them playable (or more interesting / less crippled as opponents) in the threads that follow:

http://forums.civfanatics.com/showthread.php?t=500057
http://forums.civfanatics.com/showthread.php?t=447895

The 2071 mod actually does have fully playable Natives as Nightingale said (who happen to be aliens:scan:;)) I'm not aware of mods that have implemented Natives as fully playable in the vanilla setting. However M:C is taking some steps in this direction by allowing Natives to potentially learn knowledge/techs and gradually advance to become minor civs or full-fledged civs.
 
This is a really old post, however its currently the top google search result when searching "civ 4 colonization play as native americans" so i'm posting the built-in solution.

1.) Make a multiplayer "Hotseat" game.
2.) Select a Native American country for any CPU player (not "HUMAN").
3.) Change the player type from CPU to HUMAN, for that Native American Country
4.) Remove all other HUMAN players or make them CPU Players if you want to play it as single-player (Technically its multiplayer but there is only one human player so its like a single player game.)

Enjoy, but I don't think its possible for Native American countries to win any of the victory conditions.
 
Assets\XML\Civilizations\CIV4CivilizationInfos.xml
Setting bPlayable should enable said civilization to be playable. This requires you to use a mod (or create your own) as changing the game files directly is a really bad idea as it can quickly end up breaking a lot of stuff.

Enjoy, but I don't think its possible for Native American countries to win any of the victory conditions.
In general natives are designed to be AI controlled to be resisting Europeans. They aren't intended to be played so they are missing a whole lot of gameplay features. In all honesty they are kind of boring to play. You might be able to win through as you would likely be able to trigger owning 70% of the map or whatever the number is. That is if there isn't any code to exclude victory checks for natives to save CPU time. I honestly don't know if it will even bother to test if natives have won.

I once tried playing natives in RaR (I had to modify XML to do so) and I didn't even manage to finish the first turn without the game crashing.
I never figured out why it crashed. If it had happened today, I would have investigated and figured out why it crashed and possibly fixed it. Back then I was inexperienced with the civ4col source code and I didn't have a debugger yet so it was kind of hard to do anything about.
 
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