It's because of the amount of information the server has to send you. A game like mw3 only has to send you things like the locations of players. Minecraft has to send you the locations of the players, mobs, and thousands of the blocks, between all of those things it cause Minecraft servers to have much more lag then other games do. The difference in lag is pretty big between the games, for example for a Fps that is located near me I get a ping of around 40-50 for a server located close to the other side of the world I get a ping of around 400, for a Minecraft server that is near me at best I get a ping of 400-500 due to everything it has to send. On servers that are further away it can go up to 3000+.
I'd say Mute and Homen Pigman are both right. The server's you are playing on my not be run on a powerful enough system to properly support a game with as much data as Minecraft. It could also be your own connection. Games like MW3 send very little data. Minecraft has to send millions of small bytes of data about blocks, mobs, chunks, locations of other players/mobs, world updates, the list goes on. A game like MW3 only sends data such as bullets, player locations, few entities (exploding barrels, cars, etc.), and not much else.