A lot of people are saying Zombies are a fad, but fads don't generally last almost 20 years...
Fact is, a lot of games are about shooting things. If you want to make shooting tense, you make those things monstrous and unstoppable. So, you put a story to monstrous things running around, and a context that allows you, the player, to shoot them without getting too concerned about why you are shooting them. Hmm. Alien invasion? A bit corny, and you'd probably have to end up explaining the aliens. Same with any fantasy setting, you'd have to contextualise to make the player want to shoot anything. So, its a virus, or simply the dead walking. Easy peasy. Instant drama, as humans + possibility of turning undead = plenty of story opportunity, conflict and tension with half the work of any other narrative.
Then you have to consider the gameplay. Since Evil Dead, we've associated zombies, and zombie killing, with a) hordes and b) fully customisable weapons. That is pretty much the definition of what makes an FPS fun to play, besides multiplayer. We all know the joy of splatting a zombie with the nearest thing to hand.
The reason I think its been so popular in particular with extra and downloadable content is because publishers get concerned that their game is too gritty and realistic. They want to keep that in, but they also want players to have fun with the game. What's fun, and easy to write and set up within the context of whatever your game actually is? adding "AND zombies" to every line of code, of course.
Yes, its easy. Its fun for the IKEA generation. It might seem a little tiring to some, but it'll stick around because of the sheer guilt-free joy of splatting gross-looking humans with home appliances. I agree that it can be repetitive - this is why I don't play a lot of full zombie games like Dead Rising or Resi. But I'm happy for the diversion in games such as COD or Red Dead, a nice bit of crazy gameplay as a breather between the serious stuff.
I'm not saying I agree that there isn't some alternative, somewhere, but everything I can think of to replace such joyous fully-customisable splatty carnage is basically a riff on 'zombies', but by some narrative conceit, they go by a different name - and if anything that's more irritating. That, or you go all GTA with your splatty carnage, and that's been done to death too.