It's tolerated for the same reason "free" services such as those provided by Google, Yahoo!, Facebook, and most any other important social media company display ads and do data mining on visitor and subscriber behavior. The research being conducted with the data collected in MOOCs is one of the most socially valuable results possible since it leads directly to better education for the world. As Andrew Ng has stated plainly, his primary concern in participating in Coursera is delivering the best education possible to the world's poorest people. Coursera A/B tests most every aspect of the student learning experience and makes decisions based on what results in the best student learning outcome. Exactly what better system are you proposing?