MLS has just announced that Tim Howard has been suspended for 3 games. The Rapids have issued a statement accepting the decision. I won't link the video here, but there is footage from the supporters section behind Howard's goal in KC of him telling a fan he had...relations...with the fan's mother.
3 games is in line with MLS's actions in the past around incidents like this. Colin Clark, while in Houston, got 3 games for swearing at a ball boy. Alan Gordon, while in LA, got 3 games for a homophobic slur. I'm sure a number of fans are upset with the league for this but really the only one at fault, and the only one to be upset with, is Howard. It was unprofessional and stupid and he's cost his team dearly.
UPDATE: Apparently MLS has unreleased footage of Tim getting into a physical altercation with a fan in the tunnel after the game. So, yeah, really nobody to blame on this except Tim.