NSFW obviously:
Apparently Stewart had taken Ward out a lap earlier and Ward was trying to confront him like you see sometimes in NASCAR.
Stewart then ran him over.
Who knows if he saw him in time, they both dodged the same way, or if he was going to fast - track was under caution at the time. Investigation will comment I am sure.
EDIT: It looks like some of the anger online is coming from how Stewart was going to race today anyhow but likely was pulled by the team only close to race time. Not sure how much slower you are supposed to go during caution; I almost never watch racing myself.