Sorry Lotor but the reason isn't popularity, supremism, etc.
There's actually a factual and logical reason for why people hate Elites. There's a spot on the side of Elite's necks where everything from BR bullets to sniper rounds can pass through without harming the player in question. At least this is the reason why MLG forbids the use of the Elite classification at MLG competitions or events, because it gives the user of the Elite armor classification in question an unfair advantage.
Bungie can't fix this problem with a patch so in order to repair it, they would pretty much have to release a different version of Halo 3 so they leave it the way it is.
If you don't believe me about the spot on their necks, test it yourself or watch Halo Mythbusters (I forget which episode, but it's on youtube).
I would recommend playing as a spartan, simply because I also hate Elites for the aforementioned reasoning.
Agreed as much as Ponked, that is why I do not play Team Swat anymore when I wanted to chill and have fun there were these damn elites who I would open a clip of 9 shots on and they just keep going. Try it on Guardian and see for yourself.