From what I've seen; about 80% of people hate the aliens. Why? MZ made them canon so that's not as good an excuse- besides, they have one of the best weapons for not much health to kill. It also explains why people thought they looked like that in 1950s fiction and are very interesting! My opinion anyways...
I hate Mothership Zeta. It shouldn't be considered canon at all. Mothership Zeta implies that the Great War could have been started by the aliens. That goes against the very heart of Fallout.
I don't hate the idea of Aliens in Fallout. I just hate them being a possible cause of the Great War. I hate them being a big part of the series. I hate their tech and how they could possibly change the very nature of Fallout. I hate that their tech could be handed over to Lyon's BoS if Mothership Zeta is made canon.
Aliens haven't been in Fallout before as anything other than easter eggs. Bethesda took easter eggs and made a whole DLC that just craps all over the very heart of the Fallout Universe. Aliens and their presence in the Fallout Universe will horribly unbalance everything. Turning Fallout into war of the worlds. War. War never changes... but for when Aliens attack!
Aliens as easter eggs I am ok with. Aliens having a spotlight in Fallout, having a possible cause for the Great War. Having their tech in the hands of the BoS or any other faction I HATE!
Edit: Also no Mothership Zeta isn't canon yet because it has not been mentioned in another Fallout game. It sure as hell shouldn't be made canon for reasons I already explained. The Devs of Bethesda should just say that Mothership Zeta was a "for fun DLC and wasn't meant to be canon." They really need to do that. At the very least just not mention it or have any refrences to it in an future Fallout games.