Actually, the MZ haters tend to be Alien haters in general (they see that aliens have no place in the Fallout series, and instead should live in easter-egg-land.) Also, there are several that don't like the apparent implication that they started the Great War.
And then there are those who hate it for being a half-finsihed peice of crap that was on the tailcoats of what is generally considered the best DLC for FO3. Personally? I enjoyed it, but it's a peice of crap from a technical standpoint- there's no excuse for the amount of bugs in it.
I'm one of those haters who hated it for two reasons:
One, it was a dungeon crawler with no compelling storyline. You get abducted, you join a few others and take down the ship, and you get part of the ship as a new home.
Two, It was a half-finished piece of crap.

Three, there was a holo-tape, I forget exactly which one it was, but it basically insinuated the aliens may have caused the nuclear holocaust. Which I hate, because part of Fallout is that it's mankind and all of the surviving Earth paying for it's forerunners sins.
I had no problem really with little green men, since that is a staple in pre-1950s and 1950s science fiction. But those three standpoints made me cringe at the DLC.
Who says Area 51 is only about aliens? You do know that is also where they test new and experimental aircraft right?
Also, MZ was a good DLC. Not sure what people were expecting with it.
You have to understand though that Fallout is a retrofuturistic game. While the older games were less subtle with the 1950s themes, the gameworld is designed off of the vision of the future of the denizens of the 1950s, and of 1950s science fiction. One of the thoughts during the 1950s was that Area 51 was home to alien spacecraft. If it's going to be in the game, it'll surely have something to do with aliens.
That said though, I talked to another user, Listerman about this before and we both think that if they do Area 51 it could have alien themes, but it turns out that all that alien mumbo jumbo was the American government just trying to distract the general public, and that it turns out all the alien stuff [in Area 51] was all fake. It'd be an interesting pop culture reference, and wouldn't anger people that hate the little green spacemen.