An article on the New York Times explains how a group or person was able to get malicious code inserted on the New York Times and gave readers the impression that a program was scanning their computer
New York Times Malicious Ad Code Inserted
THE NYTimes article explains that this attack via online ad systems have already hit companies like FoxNews.com and the The San Francisco Chronicle.
As you can see in the below letter from Publicis owned Starcom this is obvioulsy being taken very seriously and security is being tightened up around the ad insertion procedures...
Publicis-Starcom_Media-Partners_Letter (PDF)