re: "Two out of every three United States corporations paid no federal income taxes from 1998 through 2005"
If you take a look at the Reuters story--same day, same report--it says the corporations were ones that paid no tax for at least one year out of the seven year period. There's nothing particularly surprising about a corporation failing to make a profit for one year out of seven.
Assuming that Reuters is correct, this is a pretty dreadful case of incompetent reporting by the Times