From what I read, it was basically that EA doesn't want Valve to get anything for distributing the game, and Valve said that it was ridiculous. Basically it was that EA wants all DLC sales to be handled in-game, and Valve wants them on a seperate marketplace so they can ensure the DLC is always available right alongside the game, and that people who buy it will always have a way to access it if something should happen to their game. EA on the other hand wants Valve to foot the bill for hosting the files, but cut them entirely out of the profit for DLC, and potentially screw over customers by giving them no easy way to access DLC should the initial copy of it be lost.
Notice EA's careful wording; "BF3 will not be available on Steam as the service restricts our ability to directly support players." Notice that they try and make it about the players, because although they overwhelmingly support having the game on Steam, it's really more important that EA is able to maximize profits. This has nothing to do with the players, and is essentially politics in the Video Game Industry.
“If BF3 doesn't turn out to be the biggest selling PC shooter of all time, then I will eat my graphics card.” -MatTheCat