I do, I think it was fairly obvious to see Obsidians intentions on making them the antagonists. NCR has much more focus than the Legion, more quests and you see them more, and the NCR is sort of portrayed as the good guys, in a viewpoint that many people today (who play fallout or not) would see as being good, with their democracy and all that. That would make the NCR the protgonist.
The antagonist is just the opposition of the protaganist, the antagonist doesn't have to be evil just oppose the protagonist, whcih the Legion do quite well.
So with that said, again I think the Legion was meant to be the antagonist.
That could not be much further from the truth. By pure definition, the Legion is not the antagonist, and by definition once again, the NCR is neither a protagonist protagonist.
Making Caesar's Legion the token evil faction in FNV was never Obsidian's intention. They just didn't have time to flesh them out with more settlements and quests. Frankly, it all comes down to perspective - Nothing more.