Big Download had a chat with Tim Willis of id Software, and in that chat it's been confirmed that DOOM 4's title won't be DOOM 4, but instead it'll have a subtitle since it's not a continuation of the current DOOM story. Here's a select portion from the article:

Why did they decide to make this move? Part of the reason is that the fourth Doom game will not be a continuation of the storyline for Doom III, according to Willits. Doom III was basically a "reimagining" of the first Doom game's storyline (a la the revamped Battlestar Galactica). So willl the fourth Doom game be a continuation of, say, Doom II's Earth invasion? Willits wasn't giving up any story ideas yet.