I think it's coz it's cool to hate something popular LOL!!!!111
Naw, honestly, the bandwagon hating thing occurs in lots of pop culture, and applies to anything including games. Same reason I feel why some people hated Metallica and KoRn, and Michael Jackson, Halo and COD.
But also I think because, well to me anyways, the first time to CoD franchise exploded on the scene in this generation was CoD4: MW, and since then has done little to top that or even reach its greatness. I like spec ops in MW2, but that's about it really. I know I'm not talking for the masses, I mean the game is loved by millions and I had a thoroughly good time in all the games, but their recycling of material, and resulting fanbase are bound to expose every nuance of wrong in the games. Such as balancing, story, features and functionality, and all the rest of it.
Another thing (should've put these in point form, damn) is the overshadowing of other games that probably deserve as much accolade, but get beaten to dust and forgotten because of the CoD franchise. I liked the latest Medal of Honor, and some other more realistic shooters, which many never bother to try because of the juggernaut that is CoD.